Update:
Well, I have the game running with the boards seperated and connected via cables.
So far I have determined that the Motherboard is outputting 15khz, I have also found that the Jammit board is a video amp no matter how you have the jumpers set.
I determined this by simply bypassing the Jammit on the VGA cable. I used to have to adjust the monitor to change from my Mame setup to the orig. Site 4 setup, When I bypassed the Jammit no adjustment was needed. I fiddled with it and that's how I know it does amp the signal no matter the setting.
This is cool as I can just put in a switch run my setup using soft15khz thru the Jammit and no more hassle when switching.

Also, All communication to and from the Jammit is thru the Parallel port. If you boot the game without the Parallel cable connected the game boots to the test menu.
If you boot the game without the VGA going thru the Jammit everything works fine besides the gun reading obviously.
From looking at the board it is basically intended as a jamma 2 PC board that also adds a 3 and 4 player input, 2 lightgun inputs and stereo audio amp.
This board is what all us who want Arcade lightguns has wished for!!!
The problem is that it is unknown how this board is communicating with the PC. I was hoping I could find some port monitoring software on my Mame setup connect to the site 4 PC and Jammit and see if I could get anything interesting. I tried different setups but didn't get any results. :/
I'm fairly confident that the PC has to invoke the communication between the two.
If anyone has any knowledge about monitoring parallel ports or anything about my tinkering in general please speak up!
I am told that the reason this game is tagged not working in Mame is that the controls aren't understood. :/
I am in a unique situation where I can try and read and or write to either of the boards If I had the proper software and a clue. LOL
To show a better view of the Jammit see:
http://www.system16.com/hardware.php?id=785The Jammit is on the right obviously, the connections starting on the top right corner, left to right then going down are: Left Gun, Right Gun, Player 4, Player 3, Coinmechs, Reset.
If it were possible to figure out this board all our dreams are come true! heh
Again any insight, input anything is appreciated!
PS. Some pics for the hell of it!
The last one is my favorite, Is that not the proper way to mount a PC in a Cab or what?
Notice that all I've done so far has left the orig. hardware intact!