I'm not entirely qualified to answer, but I will answer it from what I know. There are two main differences between full JAMMA compatibility and MVS. MVS can have stereo sound instead of mono, and MVS has one extra button. From my understanding, the extra button doesn't matter in the case of MVS, but the stereo sound does. With 1 slot boards, you can switch between stereo and mono (for instance, my cab is in mono, so it is supposed to be 100% JAMMA compatible), but this is not true for 2,4 and 6 slot boards which are always stereo - I think, anyways. So to make your cab totally JAMMA compatible, you would have to make some kind of a switch to put it into mono. It's supposed to be fairly easy, but I don't know how it is done.
As far as Pac-Man goes, I believe there are some reissues or newer versions that are JAMMA, but the old ones are not - you might be able to do mods to get it to work on an old board, but I think the monitors from back then are different as well.
Marvel VS Capcom is a CPS2 board game, right? CPS2 is kind of like MVS, in that you can use what is essentially a gigantic cartridge to change games. CPS2 also has some kind of extra bit on the connector for the extra three buttons that CPS2 uses.