No idea if this is viable but I'm just going to throw this out there:
I wonder if it's be easier to make an Atomiswave Multi and then port the NAOMI games to that.
It's way more compact hardware, no I/O board needed, just regular plug and play JAMMA and the hardware costs about as much as a Capcom I/O alone.
Considering most people here seem to be interested in this because they want a more "streamlined" and easy to use NAOMI... an Atomiswave seems to better fit that goal.
Not to mention it would offer a multi solution for a piece of hardware where one doesn't already exist.