Hmm, not sure what could have caused this based on the information given. Usually almost everything metal is grounded, so if some live wire touched that it would short out, but (and someone please correct me if I'm wrong) there are fuses behind everything that goes to the playfield, so they should go first.

I figure something has shorted out one of the transformer windings, and that is causing some voltages to be out. You'll have to track down which one. I'd start by checking fuses and voltages in the backboard at least.

CPU is probably okay.

Turning the machine on is not the best idea right now, so I'll have to take back my words of checking voltages. It would indeed seem that the 13,3V winding got a short somewhere.

I would try to see if the winding itself is at least intact, maybe try measuring the resistance of that winding. If that is okay the wires need replacement. I've never had a case like this on hand, so I'd wait around for someone who has more experience to give some advice.

Maybe you can source another transformer from somewhere cheap?