After further troubleshooting I am taking a guess that it is a blown transistor on the CPU. What leads me to be belive this is the case is that there are 2 other flashers that feed into that transistor are both toast as well, it is also being shared by the knocker that I mixed up the wiring on....
Is this sound logic? I really don't know what I am doing, just reading the manual and tracing where this stuff is going on the board. I don't even know if a transistor is something that can be replaced easily, but all this stuff that is busted is going into the same thing on the board, so I am taking a wild stab that needs to be replaced, without knowing anything about this stuff at all...
so this is what being a pinball machine owner is like....