Well, after tinkering for what I thought was forever, days upon days of reading, I finally found an answer that got my trackball working
The was ONE post WAY back when, that stated that to use any other trackball than the "Special" one with the Minipac there needed to be 4 2.2k pull-up resistors placed on the outer pins and common tied to ground. One on each leg. Doing that made it work perfectly, and without a re-boot.
All of my controls came from old, gutted games like a pole position, centepede, ect... all badly damaged in one way or another. So just buying new controls for me was out of the question. But all in all, it now is working great and I can finally play Quake Arcade TE in that cab and not have a pile of "extra" wires laying about.