I had tons of issues with my Strato-Flite. It took me forever to get it 100%. But it was totally worth it. Start with the easy one. The lights on the playfield is likely the lock relay blades not making good contact. Clean the contact switches and adjust to ensure good closure and some level of overwiping.
So when the ball drains the ball index relay isn't pulling in at all by itself when you score a point?