Got things rolling again.
I now have all the chips and stuff figured out correctly. This fixed the interupts, disk read, & FIFO errors-correct boot rom (V2.7) with v3 HD & security chip.
Still had watchdog error & cmos battery low errors. New battery fixed those 2 problems.
Controls still messed up but now I have a handle on that. Something is askew in the wiring. While tracing test switch & coin door wires back I accidentally moved some wires around (I was in test mode) and it started rolling though the choices. If I hit a button it would stop until released. Then 1P joystick right would move it down when pushed. So at least it IS working, just incorrectly. I guess I'll proceed to rewire controls until I find the right one or I'm done & it works. I'll start with the harness adapters & grounds first since it worked fine before and all I did was unplug them last year. (I already checked them before but it's obviously 1 of those things that you can't just see.)
At least I know WHAT I'm looking for now. Thanks for the help guys. Hopefully I'll let you know it's working fine soon.
Pessimist: Oh, this can't get any worse!
Optimist: Yes, it can!