Known-plaintext attack on Blowfish in ECB mode
If there was a full 64-bit block of known plaintext, there would be a very fast attack using precomputation.  You can build a precomputed table of all $2^{40}$ ciphertexts.  Once you've got the precomputed table, recovering a key (given a ciphertext) would require just a single lookup in the table, so recovering a key would be extremely fast.  Storing that table would require something like 5 Terabytes of storage, which isn't too bad: it might cost you \$300 or so to buy 5 TB of storage.  The precomputation takes $2^{40}$ trial encryptions (key schedule + a single block encryption using Blowfish), e.g., 64 days for your implementation.  Once you've built the precomputed table, cracking each file/ciphertext could be done almost instantaneously.

If 5 TB of storage feels like too much, a variant of this would be to use the Hellman time-space tradeoff (or, if you prefer the "hyped" version, "rainbow tables").  That attack also requires a precomputation that takes about the same amount of time: $2^{40}$ trial encryptions.  However, its storage costs are much lower: storage for a table containing about $2^{27}$ entries (instead of $2^{40}$ entries), which corresponds to about 700 MB of storage.  The trade-off is that cracking each file/ciphertext takes a bit longer: about $2^{27}$ Blowfish trial encryptions, or about 700 seconds.  So, once you've built the precomputed table, cracking each file/ciphertext can be done very quickly: not instantaneously, but much faster than exploring the entire space of all $2^{40}$ keys.

These precomputation attacks are not of any benefit if you only have a single file to crack, but if you expect that you'll want to crack multiple files/ciphertexts, then the precomputation attacks can be beneficial: they allow you to amortize the cost of the precomputation across many different files/ciphertexts.

However, you say that you only have 32 bits of known plaintext, not a full 64-bit block of known plaintext, so these precomputation attacks are presumably not applicable to your particular setting.



FYI, the Isobe-Shibutani paper is not going to be helpful to you.  Their basic attack on reduced-round Blowfish takes at least $2^{160}$ steps of computation and thus is completely impractical -- not to mention that it only attacks a reduced-round variant of Blowfish with 8 rounds, whereas the real Blowfish uses 16 rounds.  Their attack on the full 16-round Blowfish takes $2^{288}$ steps of computation, so is ridiculously impractical.  In short: that paper is completely irrelevant to any real-world attempt to mount key-recovery attacks on Blowfish.