If you have access to a eprom writer, I suggest downloading and burning a copy of Leon's system 11 test rom. The follow the instructions for using it here:

http://pinwiki.com/wiki/index.php?title=Leon_Borre_Williams_System_11_Repair

This should at least get you started.

I am kinda in the same boat here... I accidentally sent -100 volts down the +100 volts line to my displays, and let the magic smoke out of a couple of chips on my display board, and fried the 6821 at U41 on my MPU board.

Well at a minimum you may have smoked u45. When you try to boot it, make see if the diagnostic light is blinking, this will tell you if it also took out the downstream PIA. If it is not blinking, it may be that the board is not booting at all.

A system 11 is capable of at least showing a diagnostic blink code if a PIA is out. So no boot at all may indicate a deeper problem.

You may want to start by pulling the game ROMS and going through the Worst case section of the link I posted above.

Both issues #1 and #2 could be related to U55, as it is used in both circuits. I'd replace it.

Issue #3 could could be the diode, but if it is blowing instantly, It is more likely the drive transistor on the MPU is shorted out.