Okay... the Millipede is now running...
How did I fix it so quickly you ask? I could say that I am just amazing at fixing old boards, but that would be a lie. I ended up trading the bad board + a bit of $ for a working board. While I would have loved to work on the board and fix it, I just have too many projects to do over the holiday (and most of them are not arcade related, but "keep my butt married" related.

Colors are washed out a bit, the monitor will not properly focus, but I guess I can expect that from a 25 year old game. I will order a cap kit and flyback in the new year.
Also, I cleaned out the trackball (which barely moved) and it works better, but up down is crappy. I will need to rebuild that too. (wait until I post the pictures of the crap I found inside the trackball!).