i did the same as dogp, with an extra jamma harness, diodes, a relay( to switch opto signal from the gun to each board) and a dual pole dual throw switch to direct +5 and +12 to the boardset i wanted powered on..
but like dogp, my boardsets are simular.
Not sure what headaches you will run into using dissimilar boardsets. Keep in mind also that not all boardsets sync at the same exact frequency or hav the same screen width, so while adjusting everything you may find one game needs to have a wider than normal picture to help the other game that has a narrower picture etc etc..
It would be dope if somebody cameout with a hack for the area 51 boardset to have lots of different shooter games... that would be sweet.