Holly (since you asked the original question)
Indeed the Hyper Neo Geo 64 is basically the same pinout as the Neo Geo MVS. There are two versions of the NG64, the first version is the one you are thinking of that requires an extra power connector to the board. The second version should be able to draw the power it needs from the JAMMA edge connector.
I don't know much about the Atomiswave as I don't have one of those.
(Edit: Atomiswave manual here:
https://wiki.arcadeotaku.com/images/9/9e/Atomiswave_manual.pdf , the fourth button is in the same place as the MVS it looks like, with the fifth button next to it on the connector. I guess I never realized that the Atomiswave has a standard JAMMA connector on it, I have a Naomi/Naomi 2 which follows the JVS standard and requires an I/O board to connect to a JAMMA cabinet.)
It seems that recently a technique has been developed to reprogram the encryption keys stored in the battery backed up RAM, so there's no need to run modified "phoenixed" ROM sets. If you're concerned with getting original cartridges you still have to be on the lookout for conversions (from a common game to a rare game), though.
Well...you still need a Supergun or similar thing to power the board and connect joysticks. JAMMA boards output RGB video by default so you should be OK there but you'd need to have controllers and a way to hook them up of course. They aren't that hard to build if you're inclined to do that sort of thing.
There are also consolized CPS2 boards out there (see the UD CPS2 here:
http://udgametech.blogspot.com/) that use a laptop power supply and have USB ports for joysticks and A/V output via the old PlayStation analog connector. If you are really only interested in CPS2 that would be one way to go although I dunno how hard it is to get one these days.