Here's the finished version of the supergun hooked into my neo geo

basic jamma buttons hook up through sega genesis ports. Extended buttons I wired into usb ports. Audio I rigged into stereo headphone jacks. I also set up the sound circuits so they work on my amp and speakers (nice and loud yay). As you can see the neo geo case has a stereo sound plug on it because I get stereo sound out of headphone pins from my mvs board.
Here's the controllers I'm using on it

the limited street fighter stick I swapped out the joystick with one from a x-arcade because it has a shorter throw.
Here's the rgb to s-video encoding part of it. I used scart parts for it so I can also use it on my consoles like my megadrive and my super famicom. I rigged the power to the encoder board into the same psu that powers the supergun.

The encoder board itself is just one of these
http://cgi.ebay.com/Arcade-RGB-CGA-to-T ... 240%3A1318
I modded the s-video cord hooked into it to fix the oversaturated colours.
Here's a closeup of what's going on inside the jamma connector box

Modified vogatek mark 1 with all the bells and whistles. Soldered usb ports onto the 4th neo geo button pins. And also soldered a spare button that lets me get into the bios menu. Did a couple of other modifications to fix video sync and audio