I don't mean to sound harsh but have dyslexia and in a rush.
You need to post your pic's here and not on an external site. People are less likely to take the extra step to help.
To post photo's click on the attachments and other options and look at my attached pic.
Is that a regular x86 intel CPU mother board? How is the Jamma connectioned to the mother board (pic)? There are JAMMA switchers out there that will let you have two boards in one arcade but I have never used one and I have no idea if one would help you. It's hard to even try to think it out with out pics.
If you have GroovyMame questions you will probably get a quicker reply by posting you questions in the GroovyMame section.
http://forum.arcadecontrols.com/index.php/board,52.0.htmlEdit: I went and looked closer at you externally linked pic's. I see what you mean about the JAMMA board to USB. I think you could do a JAMMA switching board and just add a second PC with something like a jpac for MAME, but I have never used either and would not be the person to ask.
http://www.ebay.com/itm/2-in-1-Multi-JAMMA-Switcher-PCB-Arcade-Game-2-in-1-Switch-Control-JAMMA-PC-Board-/331132529126http://www.ultimarc.com/jpac.htmlI'd do a some reading on them and start a new topic under the Mane topic about adding one and if it would work for what you want.
If you start a topic about an ultimarc product with the name of the item in the name of the thread, Some one who has one or Andy from ultimarc will probably respond to your questions. Just do your reading about the product first.