I use a seperate adapter to connect my MiSTer to JAMMA via the VGA, which was powering the MiSTer. This breakout works great (even with my adapter) but the MiSTer can no longer receive power through VGA, so I had to reintroduce a seperate power cord (no big deal). Works flawlessly and laglessly as best as I can tell.
I did not make any modifications to my .ini file and it worked immediately with my 3rd party Guncon 2.
Thank you!