Wellp,
The MVS standard is not exactly JAMMA, but close. It has an extra couple of buttons and stuff. Atomiswave calls for 5 buttons by default IIIRC. Basically you'd probably have to customize/rewire the harness abit. Atomiswave also uses a 31khz display by default I believe, so you would need a new monitor to get the best out of it, but I'm pretty sure it also has a 15khz compatibility mode.