I got version 2.00 working now, thanks to Zak for posting the data!

Just played through it and...it just ends after level 4? Is there some sort of criteria you need to satisfy to get to the final stage? I was credit feeding so maybe that's it although I credit fed all the way through all 5 levels in version 4.00 earlier.
Also, this version only has 2 playable characters instead of 4. There's probably other differences but I'm no expert at the game so I can't say what.
I needed to hack the .exe to get it to work, and it turns out the offsets are different from version 4.00. I was able to find the correct values to alter based on searching through the binary and matching the hex strings with those of version 4.00, although it was non-trivial to find them.
Anyway, here are the addresses to alter in version 2.00 to skip the key check:
40630: 74 EB
48B47: 72 EB
A43AD: 0F E9
A43AE: 84 CF
A43AF: CE 00
A43B2: 00 90
A46A4: 74 EB
Note: you still need the dongle attached for it to run, it just doesn't matter if the key on it matches your i/o board or not.