When I originally wrote the key searching program, that was on the assumption that the key for the second Feistel network was 96 bits long.
Each (E,D) pair reduces the key space by a factor of about 216, so to isolate the correct key with good confidence one would need at least 96/16 = 6 (E,D) pairs.
The big problem is finding those pairs. Remember that they must be at compatible addresses, that is addresses whose bottom 17 bits are the same. This is a serious limitation, because the code of several games only covers a range of 0x80000 bytes, which would give a maximum of 4 pairs at any address. For the Super Puzzle Fighter 2 games, the range is just 0x40000 bytes, giving just 2 pairs per address.
One can find hundreds, even thousands of of (E,D) pairs, but if they are not at compatible addresses they are of no use to find the key using this attack.
However, now we know that the key actually has only 64 significant bits, some of which are repeated. I therefore rewrote the program to take that into account. This means that only 4 (E,D) pairs are needed to isolate the key.
Also, I made several important optimisations that I missed the first time around, like caching intermediate results and speeding up the s-boxes calculations by using precalculated tables (this last optimisation also made into MAME so the decryption when loading a game is now faster).
The end result is a program that is orders of magnitude faster than the previous one.
Now it takes just 15 seconds to find the key given 8 (E,D) pairs. With 5 pairs, which was just plain impossible before, it takes 5 minutes. With 4 pairs, 35 minutes.
These improvement made it simple to find most of the remaining keys, even for games that didn't have a matching revision already decrypted (most notably some of the Steeet Fighter Zero versions).
But there's more: the program is now fast enough to go one step further, and look for the key with just 3 pairs. Of course 3 pairs are not enough to isolate the right key: they only reduce the key space by about 248, therefore leaving about 216 keys which are compatible with the data. Once a 64-bit key for the second Feistel network is selected, the compatible 64-bit master keys can then be easily generated, and used to verify other (E,D) pairs at different addresses. This allows to find the correct key in less than one day, and I had to use this extended attack for a couple of the most problematic games.
In the meantime, Andreas Naive has been busy implementing the attack he had described on his blog, and was able to find the keys for two of the Super Puzzle Fighter 2 games. Unfortunately, the attack failed on the third. Work is still in progress on that one, and there is some hope that the key will eventually be found.
The only other games that are missing a key are the two CPS2 versions of Mega Man. There is no decrypted CPS2 version of that game to compare with, and the CPS1 version seems to be too different to be able to find good pairs.