Using similar passwords and salts for PBKDF2
If there would be risk from related inputs one would know that because then HMAC would be target to chosen plaintext attacks and hence PBKDF2 would have been fully obsolete. So there's no weakness in using related inputs.
As each cell basically has a different password there's no faster way than brute-force to find out the values. However, if you know how the mapping takes place and you broke r1 and r2, one can fastly calculate the other entries (as fast as the defender did, as there's no entropy left)
I'd suggest you to increase the iteration count to 1000000 as this is far more secure and still takes less than a second on most pcs.
16 bytes for the r-values suffices, if you got "high entropy" in them (80 bits + -> >6 bits per byte)
As pointed out correctly in the comments, PBKDF2 is not a viable choice for password hashing. Rather use scrypt or the winner of the PHC (announced within next two months)