Structuring Large Quartus Projects
DES has a complexity of around 4700 gate equivalents.  It's kind of small to be worrying about testing individual 'modules'.  

DES historically was intended to only be implemented in hardware and the specification describes connectivity and order. 

The Initial Permutation and Inverse Initial Permutation describe an 8 bit interface delivering ordered bits to and from two 32 bit registers (comprised of four 8 bit shift registers, that can be parallel read and loaded during rounds):



Initial Permutation



Inverse Initial Permutation

Note that barring LR and RL order the IP and IP-1 are symmetrical.  It isn't necessary to test them individually, even depending on using a different interface size.  There are known value tests that provide complete coverage for DES and allow a high degree of fault isolation, these could be used for BIST.

Permuted Choice 1 tells a similar tale to the Initial Permutation for loading key from an 8 bit interface into the C and D registers comprised of three 8 bit and one 4 bit left and right shifting registers with parallel output (for PC2):



And up to this point we've dealt with a total of 25 wires if you were to use an 8 bit wide interface. Regardless of the interface size, you can test those 25 or upto 184 wires with marching '1's, as long as you can observe the results externally.

Permuted Choice 2 describes tap off ordering from the C and D registers to produce a selected key for each round:

 

Permuted Choice 2

You can minimize the impact of the key by setting it to all '0's while testing other elements.  DES can be completely tested in 291 vectors comprised of a 64 bit key value (including parity), a 64 bit input value, a 64 bit output value and a bit describing the encryption/decryption mode of a particular vector.  Further the tests are ordered so you don't need redundant information:

# Test vectors for DES Electronic Code Book (ECB)
# implementation, derived from:
#   "Validating the Correctness of Hardware 
#   Implementations of the NBS Data Encryption Standard"
#   NBS Special Publication 500-20, 1980.
#
#    Initial Permutation and Expansion test
#
encrypt
#
 0101010101010101 95F8A5E5DD31D900 8000000000000000
 0101010101010101 DD7F121CA5015619 4000000000000000
 0101010101010101 2E8653104F3834EA 2000000000000000
 0101010101010101 4BD388FF6CD81D4F 1000000000000000
 0101010101010101 20B9E767B2FB1456 0800000000000000
 0101010101010101 55579380D77138EF 0400000000000000
 0101010101010101 6CC5DEFAAF04512F 0200000000000000
 0101010101010101 0D9F279BA5D87260 0100000000000000
 0101010101010101 D9031B0271BD5A0A 0080000000000000
 0101010101010101 424250B37C3DD951 0040000000000000
 0101010101010101 B8061B7ECD9A21E5 0020000000000000
 0101010101010101 F15D0F286B65BD28 0010000000000000
 0101010101010101 ADD0CC8D6E5DEBA1 0008000000000000
 0101010101010101 E6D5F82752AD63D1 0004000000000000
 0101010101010101 ECBFE3BD3F591A5E 0002000000000000
 0101010101010101 F356834379D165CD 0001000000000000
 0101010101010101 2B9F982F20037FA9 0000800000000000
 0101010101010101 889DE068A16F0BE6 0000400000000000
 0101010101010101 E19E275D846A1298 0000200000000000
 0101010101010101 329A8ED523D71AEC 0000100000000000
 0101010101010101 E7FCE22557D23C97 0000080000000000
 0101010101010101 12A9F5817FF2D65D 0000040000000000
 0101010101010101 A484C3AD38DC9C19 0000020000000000
 0101010101010101 FBE00A8A1EF8AD72 0000010000000000
 0101010101010101 750D079407521363 0000008000000000
 0101010101010101 64FEED9C724C2FAF 0000004000000000
 0101010101010101 F02B263B328E2B60 0000002000000000
 0101010101010101 9D64555A9A10B852 0000001000000000
 0101010101010101 D106FF0BED5255D7 0000000800000000
 0101010101010101 E1652C6B138C64A5 0000000400000000
 0101010101010101 E428581186EC8F46 0000000200000000
 0101010101010101 AEB5F5EDE22D1A36 0000000100000000
 0101010101010101 E943D7568AEC0C5C 0000000080000000
 0101010101010101 DF98C8276F54B04B 0000000040000000
 0101010101010101 B160E4680F6C696F 0000000020000000
 0101010101010101 FA0752B07D9C4AB8 0000000010000000
 0101010101010101 CA3A2B036DBC8502 0000000008000000
 0101010101010101 5E0905517BB59BCF 0000000004000000
 0101010101010101 814EEB3B91D90726 0000000002000000
 0101010101010101 4D49DB1532919C9F 0000000001000000
 0101010101010101 25EB5FC3F8CF0621 0000000000800000
 0101010101010101 AB6A20C0620D1C6F 0000000000400000
 0101010101010101 79E90DBC98F92CCA 0000000000200000
 0101010101010101 866ECEDD8072BB0E 0000000000100000
 0101010101010101 8B54536F2F3E64A8 0000000000080000
 0101010101010101 EA51D3975595B86B 0000000000040000
 0101010101010101 CAFFC6AC4542DE31 0000000000020000
 0101010101010101 8DD45A2DDF90796C 0000000000010000
 0101010101010101 1029D55E880EC2D0 0000000000008000
 0101010101010101 5D86CB23639DBEA9 0000000000004000
 0101010101010101 1D1CA853AE7C0C5F 0000000000002000
 0101010101010101 CE332329248F3228 0000000000001000
 0101010101010101 8405D1ABE24FB942 0000000000000800
 0101010101010101 E643D78090CA4207 0000000000000400
 0101010101010101 48221B9937748A23 0000000000000200
 0101010101010101 DD7C0BBD61FAFD54 0000000000000100
 0101010101010101 2FBC291A570DB5C4 0000000000000080
 0101010101010101 E07C30D7E4E26E12 0000000000000040
 0101010101010101 0953E2258E8E90A1 0000000000000020
 0101010101010101 5B711BC4CEEBF2EE 0000000000000010
 0101010101010101 CC083F1E6D9E85F6 0000000000000008
 0101010101010101 D2FD8867D50D2DFE 0000000000000004
 0101010101010101 06E7EA22CE92708F 0000000000000002
 0101010101010101 166B40B44ABA4BD6 0000000000000001
#
#    Inverse Permutation and Expansion test 
#
encrypt
#
 0101010101010101 8000000000000000 95F8A5E5DD31D900
 0101010101010101 4000000000000000 DD7F121CA5015619
 0101010101010101 2000000000000000 2E8653104F3834EA
 0101010101010101 1000000000000000 4BD388FF6CD81D4F
 0101010101010101 0800000000000000 20B9E767B2FB1456
 0101010101010101 0400000000000000 55579380D77138EF
 0101010101010101 0200000000000000 6CC5DEFAAF04512F
 0101010101010101 0100000000000000 0D9F279BA5D87260
 0101010101010101 0080000000000000 D9031B0271BD5A0A
 0101010101010101 0040000000000000 424250B37C3DD951
 0101010101010101 0020000000000000 B8061B7ECD9A21E5
 0101010101010101 0010000000000000 F15D0F286B65BD28
 0101010101010101 0008000000000000 ADD0CC8D6E5DEBA1
 0101010101010101 0004000000000000 E6D5F82752AD63D1
 0101010101010101 0002000000000000 ECBFE3BD3F591A5E
 0101010101010101 0001000000000000 F356834379D165CD
 0101010101010101 0000800000000000 2B9F982F20037FA9
 0101010101010101 0000400000000000 889DE068A16F0BE6
 0101010101010101 0000200000000000 E19E275D846A1298
 0101010101010101 0000100000000000 329A8ED523D71AEC
 0101010101010101 0000080000000000 E7FCE22557D23C97
 0101010101010101 0000040000000000 12A9F5817FF2D65D
 0101010101010101 0000020000000000 A484C3AD38DC9C19
 0101010101010101 0000010000000000 FBE00A8A1EF8AD72
 0101010101010101 0000008000000000 750D079407521363
 0101010101010101 0000004000000000 64FEED9C724C2FAF
 0101010101010101 0000002000000000 F02B263B328E2B60
 0101010101010101 0000001000000000 9D64555A9A10B852
 0101010101010101 0000000800000000 D106FF0BED5255D7
 0101010101010101 0000000400000000 E1652C6B138C64A5
 0101010101010101 0000000200000000 E428581186EC8F46
 0101010101010101 0000000100000000 AEB5F5EDE22D1A36
 0101010101010101 0000000080000000 E943D7568AEC0C5C
 0101010101010101 0000000040000000 DF98C8276F54B04B
 0101010101010101 0000000020000000 B160E4680F6C696F
 0101010101010101 0000000010000000 FA0752B07D9C4AB8
 0101010101010101 0000000008000000 CA3A2B036DBC8502
 0101010101010101 0000000004000000 5E0905517BB59BCF
 0101010101010101 0000000002000000 814EEB3B91D90726
 0101010101010101 0000000001000000 4D49DB1532919C9F
 0101010101010101 0000000000800000 25EB5FC3F8CF0621
 0101010101010101 0000000000400000 AB6A20C0620D1C6F
 0101010101010101 0000000000200000 79E90DBC98F92CCA
 0101010101010101 0000000000100000 866ECEDD8072BB0E
 0101010101010101 0000000000080000 8B54536F2F3E64A8
 0101010101010101 0000000000040000 EA51D3975595B86B
 0101010101010101 0000000000020000 CAFFC6AC4542DE31
 0101010101010101 0000000000010000 8DD45A2DDF90796C
 0101010101010101 0000000000008000 1029D55E880EC2D0
 0101010101010101 0000000000004000 5D86CB23639DBEA9
 0101010101010101 0000000000002000 1D1CA853AE7C0C5F
 0101010101010101 0000000000001000 CE332329248F3228
 0101010101010101 0000000000000800 8405D1ABE24FB942
 0101010101010101 0000000000000400 E643D78090CA4207
 0101010101010101 0000000000000200 48221B9937748A23
 0101010101010101 0000000000000100 DD7C0BBD61FAFD54
 0101010101010101 0000000000000080 2FBC291A570DB5C4
 0101010101010101 0000000000000040 E07C30D7E4E26E12
 0101010101010101 0000000000000020 0953E2258E8E90A1
 0101010101010101 0000000000000010 5B711BC4CEEBF2EE
 0101010101010101 0000000000000008 CC083F1E6D9E85F6
 0101010101010101 0000000000000004 D2FD8867D50D2DFE
 0101010101010101 0000000000000002 06E7EA22CE92708F
 0101010101010101 0000000000000001 166B40B44ABA4BD6
#
#   Key Permutation tests
#
encrypt
#
 8001010101010101 0000000000000000 95A8D72813DAA94D
 4001010101010101 0000000000000000 0EEC1487DD8C26D5
 2001010101010101 0000000000000000 7AD16FFB79C45926
 1001010101010101 0000000000000000 D3746294CA6A6CF3
 0801010101010101 0000000000000000 809F5F873C1FD761
 0401010101010101 0000000000000000 C02FAFFEC989D1FC
 0201010101010101 0000000000000000 4615AA1D33E72F10
 0180010101010101 0000000000000000 2055123350C00858
 0140010101010101 0000000000000000 DF3B99D6577397C8
 0120010101010101 0000000000000000 31FE17369B5288C9
 0110010101010101 0000000000000000 DFDD3CC64DAE1642
 0108010101010101 0000000000000000 178C83CE2B399D94
 0104010101010101 0000000000000000 50F636324A9B7F80
 0102010101010101 0000000000000000 A8468EE3BC18F06D
 0101800101010101 0000000000000000 A2DC9E92FD3CDE92
 0101400101010101 0000000000000000 CAC09F797D031287
 0101200101010101 0000000000000000 90BA680B22AEB525
 0101100101010101 0000000000000000 CE7A24F350E280B6
 0101080101010101 0000000000000000 882BFF0AA01A0B87
 0101040101010101 0000000000000000 25610288924511C2
 0101020101010101 0000000000000000 C71516C29C75D170
 0101018001010101 0000000000000000 5199C29A52C9F059
 0101014001010101 0000000000000000 C22F0A294A71F29F
 0101012001010101 0000000000000000 EE371483714C02EA
 0101011001010101 0000000000000000 A81FBD448F9E522F
 0101010801010101 0000000000000000 4F644C92E192DFED
 0101010401010101 0000000000000000 1AFA9A66A6DF92AE
 0101010201010101 0000000000000000 B3C1CC715CB879D8
 0101010180010101 0000000000000000 19D032E64AB0BD8B
 0101010140010101 0000000000000000 3CFAA7A7DC8720DC
 0101010120010101 0000000000000000 B7265F7F447AC6F3
 0101010110010101 0000000000000000 9DB73B3C0D163F54
 0101010108010101 0000000000000000 8181B65BABF4A975
 0101010104010101 0000000000000000 93C9B64042EAA240
 0101010102010101 0000000000000000 5570530829705592
 0101010101800101 0000000000000000 8638809E878787A0
 0101010101400101 0000000000000000 41B9A79AF79AC208
 0101010101200101 0000000000000000 7A9BE42F2009A892
 0101010101100101 0000000000000000 29038D56BA6D2745
 0101010101080101 0000000000000000 5495C6ABF1E5DF51
 0101010101040101 0000000000000000 AE13DBD561488933
 0101010101020101 0000000000000000 024D1FFA8904E389
 0101010101018001 0000000000000000 D1399712F99BF02E
 0101010101014001 0000000000000000 14C1D7C1CFFEC79E
 0101010101012001 0000000000000000 1DE5279DAE3BED6F
 0101010101011001 0000000000000000 E941A33F85501303
 0101010101010801 0000000000000000 DA99DBBC9A03F379
 0101010101010401 0000000000000000 B7FC92F91D8E92E9
 0101010101010201 0000000000000000 AE8E5CAA3CA04E85
 0101010101010180 0000000000000000 9CC62DF43B6EED74
 0101010101010140 0000000000000000 D863DBB5C59A91A0
 0101010101010120 0000000000000000 A1AB2190545B91D7
 0101010101010110 0000000000000000 0875041E64C570F7
 0101010101010108 0000000000000000 5A594528BEBEF1CC
 0101010101010104 0000000000000000 FCDB3291DE21F0C0
 0101010101010102 0000000000000000 869EFD7F9F265A09
#
#   Test of right-shifts in Decryption
#
decrypt
#
 8001010101010101 95A8D72813DAA94D 0000000000000000
 4001010101010101 0EEC1487DD8C26D5 0000000000000000
 2001010101010101 7AD16FFB79C45926 0000000000000000
 1001010101010101 D3746294CA6A6CF3 0000000000000000
 0801010101010101 809F5F873C1FD761 0000000000000000
 0401010101010101 C02FAFFEC989D1FC 0000000000000000
 0201010101010101 4615AA1D33E72F10 0000000000000000
 0180010101010101 2055123350C00858 0000000000000000
 0140010101010101 DF3B99D6577397C8 0000000000000000
 0120010101010101 31FE17369B5288C9 0000000000000000
 0110010101010101 DFDD3CC64DAE1642 0000000000000000
 0108010101010101 178C83CE2B399D94 0000000000000000
 0104010101010101 50F636324A9B7F80 0000000000000000
 0102010101010101 A8468EE3BC18F06D 0000000000000000
 0101800101010101 A2DC9E92FD3CDE92 0000000000000000
 0101400101010101 CAC09F797D031287 0000000000000000
 0101200101010101 90BA680B22AEB525 0000000000000000
 0101100101010101 CE7A24F350E280B6 0000000000000000
 0101080101010101 882BFF0AA01A0B87 0000000000000000
 0101040101010101 25610288924511C2 0000000000000000
 0101020101010101 C71516C29C75D170 0000000000000000
 0101018001010101 5199C29A52C9F059 0000000000000000
 0101014001010101 C22F0A294A71F29F 0000000000000000
 0101012001010101 EE371483714C02EA 0000000000000000
 0101011001010101 A81FBD448F9E522F 0000000000000000
 0101010801010101 4F644C92E192DFED 0000000000000000
 0101010401010101 1AFA9A66A6DF92AE 0000000000000000
 0101010201010101 B3C1CC715CB879D8 0000000000000000
 0101010180010101 19D032E64AB0BD8B 0000000000000000
 0101010140010101 3CFAA7A7DC8720DC 0000000000000000
 0101010120010101 B7265F7F447AC6F3 0000000000000000
 0101010110010101 9DB73B3C0D163F54 0000000000000000
 0101010108010101 8181B65BABF4A975 0000000000000000
 0101010104010101 93C9B64042EAA240 0000000000000000
 0101010102010101 5570530829705592 0000000000000000
 0101010101800101 8638809E878787A0 0000000000000000
 0101010101400101 41B9A79AF79AC208 0000000000000000
 0101010101200101 7A9BE42F2009A892 0000000000000000
 0101010101100101 29038D56BA6D2745 0000000000000000
 0101010101080101 5495C6ABF1E5DF51 0000000000000000
 0101010101040101 AE13DBD561488933 0000000000000000
 0101010101020101 024D1FFA8904E389 0000000000000000
 0101010101018001 D1399712F99BF02E 0000000000000000
 0101010101014001 14C1D7C1CFFEC79E 0000000000000000
 0101010101012001 1DE5279DAE3BED6F 0000000000000000
 0101010101011001 E941A33F85501303 0000000000000000
 0101010101010801 DA99DBBC9A03F379 0000000000000000
 0101010101010401 B7FC92F91D8E92E9 0000000000000000
 0101010101010201 AE8E5CAA3CA04E85 0000000000000000
 0101010101010180 9CC62DF43B6EED74 0000000000000000
 0101010101010140 D863DBB5C59A91A0 0000000000000000
 0101010101010120 A1AB2190545B91D7 0000000000000000
 0101010101010110 0875041E64C570F7 0000000000000000
 0101010101010108 5A594528BEBEF1CC 0000000000000000
 0101010101010104 FCDB3291DE21F0C0 0000000000000000
 0101010101010102 869EFD7F9F265A09 0000000000000000
#
#   Data permutation test
#
encrypt
#
 1046913489980131 0000000000000000 88D55E54F54C97B4
 1007103489988020 0000000000000000 0C0CC00C83EA48FD
 10071034C8980120 0000000000000000 83BC8EF3A6570183
 1046103489988020 0000000000000000 DF725DCAD94EA2E9
 1086911519190101 0000000000000000 E652B53B550BE8B0
 1086911519580101 0000000000000000 AF527120C485CBB0
 5107B01519580101 0000000000000000 0F04CE393DB926D5
 1007B01519190101 0000000000000000 C9F00FFC74079067
 3107915498080101 0000000000000000 7CFD82A593252B4E
 3107919498080101 0000000000000000 CB49A2F9E91363E3
 10079115B9080140 0000000000000000 00B588BE70D23F56
 3107911598080140 0000000000000000 406A9A6AB43399AE
 1007D01589980101 0000000000000000 6CB773611DCA9ADA
 9107911589980101 0000000000000000 67FD21C17DBB5D70
 9107D01589190101 0000000000000000 9592CB4110430787
 1007D01598980120 0000000000000000 A6B7FF68A318DDD3
 1007940498190101 0000000000000000 4D102196C914CA16
 0107910491190401 0000000000000000 2DFA9F4573594965
 0107910491190101 0000000000000000 B46604816C0E0774
 0107940491190401 0000000000000000 6E7E6221A4F34E87
 19079210981A0101 0000000000000000 AA85E74643233199
 1007911998190801 0000000000000000 2E5A19DB4D1962D6
 10079119981A0801 0000000000000000 23A866A809D30894
 1007921098190101 0000000000000000 D812D961F017D320
 100791159819010B 0000000000000000 055605816E58608F
 1004801598190101 0000000000000000 ABD88E8B1B7716F1
 1004801598190102 0000000000000000 537AC95BE69DA1E1
 1004801598190108 0000000000000000 AED0F6AE3C25CDD8
 1002911498100104 0000000000000000 B3E35A5EE53E7B8D
 1002911598190104 0000000000000000 61C79C71921A2EF8
 1002911598100201 0000000000000000 E2F5728F0995013C
 1002911698100101 0000000000000000 1AEAC39A61F0A464
#
#   S-Box test
#
encrypt
#
 7CA110454A1A6E57 01A1D6D039776742 690F5B0D9A26939B
 0131D9619DC1376E 5CD54CA83DEF57DA 7A389D10354BD271
 07A1133E4A0B2686 0248D43806F67172 868EBB51CAB4599A
 3849674C2602319E 51454B582DDF440A 7178876E01F19B2A
 04B915BA43FEB5B6 42FD443059577FA2 AF37FB421F8C4095
 0113B970FD34F2CE 059B5E0851CF143A 86A560F10EC6D85B
 0170F175468FB5E6 0756D8E0774761D2 0CD3DA020021DC09
 43297FAD38E373FE 762514B829BF486A EA676B2CB7DB2B7A
 07A7137045DA2A16 3BDD119049372802 DFD64A815CAF1A0F
 04689104C2FD3B2F 26955F6835AF609A 5C513C9C4886C088
 37D06BB516CB7546 164D5E404F275232 0A2AEEAE3FF4AB77
 1F08260D1AC2465E 6B056E18759F5CCA EF1BF03E5DFA575A
 584023641ABA6176 004BD6EF09176062 88BF0DB6D70DEE56
 025816164629B007 480D39006EE762F2 A1F9915541020B56
 49793EBC79B3258F 437540C8698F3CFA 6FBF1CAFCFFD0556
 4FB05E1515AB73A7 072D43A077075292 2F22E49BAB7CA1AC
 49E95D6D4CA229BF 02FE55778117F12A 5A6B612CC26CCE4A
 018310DC409B26D6 1D9D5C5018F728C2 5F4C038ED12B2E41
 1C587F1C13924FEF 305532286D6F295A 63FAC0D034D9F793


(There may or may not be a parity error in one vector)

You might gather I've done at least one VHDL implementation.  How the design hierarchy is organized is dependent on the interface bus width and how efficiently the DES algorithm executes (pre-scheduled keys, superscalar pipelining, ...).  The 8 bit interface design model took about 2 1/2 days to implement and debug (having had experience writing C programs for implementing DES).



Addendum

From the following list of vhdl source files for a simple DES implementation:

bidir.vhdl           encrypt_vector.vhdl  sbox3.vhdl
cd_reg.vhdl          inbuf.vhdl           sbox4.vhdl
cipher_vector.vhdl   invbuf.vhdl          sbox5.vhdl
clkbuf.vhdl          key_vector.vhdl      sbox6.vhdl
des.vhdl             outbuf.vhdl          sbox7.vhdl
des_tb.vhdl          plain_vector.vhdl    sbox8.vhdl
dslice0.vhdl         reg6.vhdl            sr4.vhdl
dslice1.vhdl         reg8s.vhdl           sr8.vhdl
dslice2.vhdl         sbox1.vhdl           statem.vhdl
dslice3.vhdl         sbox2.vhdl


You can get that this is an instantiated RTL model of the actual hardware.  In an FPGA implementation the buffer models wouldn't be used.  There's a top level test bench (des_tb.vhdl) that performs design validation, while synthesis starts at the top of the actual design (des.vhdl), which uses an 8 bit interface.  The hierarchy is shown (with duplicate implementations removed)

work.des_tb (behave)

work.key_vector (behave)
work.plain_vector (behave)
work.cipher_vector (behave)
work.encrypt_vector (behave)
work.des (behave)

    work.bidir (behave)
    work.clkbuf (behave)
    work.invbuf (behave)
    work.inbuf (behave)
    work.outbuf (behave)
    work.statem (behave)

        work.reg6 (behave)

    work.dslice0 (behave)

        work.reg8s (behave)
        work.sbox1 (behave)
        work.sbox2 (behave)

    work.dslice1 (behave)

        work.reg8s (behave)
        work.sbox3 (behave)
        work.sbox4 (behave)

    work.cd_reg (behave)

        work.sr8 (behave)
        work.sr4 (behave)

    work.dslice2 (behave)

        work.reg8s (behave)
        work.sbox5 (behave)
        work.sbox6 (behave)

    work.dslice3 (behave)

        work.reg8s (behave)
        work.sbox7 (behave)
        work.sbox8 (behave)


The dslice elements are uniquified by S Box, and the organization is based on length of and number (locality) of wires (nets), in an organization seen in the first commercially available DES implementation (Fairchild 8414, four 40 pin bipolar chips each containing a byte of L, a byte of R, three bytes and a nybble of either C and D, and two masked S Box ROMs.

DES was originally specified to be implemented in hardware and VHDL is ideally suited for hardware description, while FIPS PUB 46 is an interoperability standard and not an implementation standard.  Writing a VHDL model based on the interoperability standard, which isn't too bad from a software perspective can end up with a complex VHDL description that actually results in simple hardware (see the P. Ghosal paper's link (in comments) Table 1.  In general we test connectivity in permutations that are simply wires, not their description accuracy, which is a text domain issue.

The state machine implements the Key Schedule, in this simple implementation by shifting the C and D registers either right or left by either one or two clocks before the next round of L and R are latched (registered).

So the point of this is two fold.  First DES is simple in terms of hardware.  The entire model including the test bench implemented entirely using signals ends up with 473 signals, including hierarchical represented distinct VHDL drivers.  It wouldn't be that far off from a 64 bit interface implementation.  Second that what we should be testing in a hardware design language is the accuracy of the resulting hardware, and not whether there are transcription errors modeling permutations like software.

You could test hierarchical design units separately.  In this case the complexity is low enough that's not really needed.  If I were going to write design units for permutations, I'd write C programs to translate tables for a known good C implementation of DES into VHDL (which is how the S Boxes are done here, although I did four different implementations, from  LUTs to logic, to reduced complexity ROMs).

I also wrote a C Program to convert the 291 test vectors from NBS Special Pub 500-20 to VHDL, organized as key vectors, input vectors (plain), and output vectors (cipher, expected results).

In the case of testing permutations as design units separately, you could write a C program that generated thorough test cases as VHDL along with expected results and provide individual test benches.