audio sources tend to be very forgiving, since you should only have one or the other on at a time.
I picture it like this although id actually have to build it and work out the bugs to see if their are any ill effects.
i would get a Jpac for the pc interface.
simple reason is that you can go through the jamma setup.
what id do then is id get an additional jamma harness, and splice it into your cabinet jamma harness about 6 inches from the jamma connector, wire for wire.
that way you would have one jamma plug going to the jpac, and one going to the naomi. since the jpac has no physical connections on the board for the jamma power supply, you should be ok in that area.
also, running through the jpac you shouldnt need an arcadevga card.
get a dpdt switch with center off and wire that in so if you flip the switch one way, the naomi is powered up and if you flip it the other way it acts just like a regular mame cabinet.
you also would need to leave in the jamma power supply, and then have a seperate ATX or ATX 2 supply. this is the simplest way to do it.
hey let me know how it works if you try it.