Just to close out this thread...
Alan checked and repaired all my broken PC boards. I re-installed and still have issues. We've determined it's the wiring. To be honest, this has been, by far, the most difficult machine to work on for me. I think half the problem is that I'm horrible with tracing wiring issues and there's a lot here. I have one more area to check, removing the small board next to the hopper plug to check, where Alan told me to look at a delay relay.
If this isn't the issue I'm going to mothball the machine and just drive it out to K-LAR! I need a vacation anyway and I actually enjoy driving out to the desert, once I get over the Cajon pass of course.