Quoted from frunch:
Glad to see you finally reached the end of this saga! One suggestion regarding the scoring issue--if you suspect it's switch related, make sure to replace the capacitors on any switches that use them. I've seen weird switch behavior come from old, faulty switch caps.
Thanks. The double scoring was due to the outhole switch #1. When there was only one ball left in the trough, 1 ball locked in a Saucer and one ball in play, the ball in the trough touching the outhole switch would vibrate and move from the Flippers being active. It was just enough vibration to make the ball roll off the switch and the switch wasn't depressed enough. A slight adjustment to the wire on the switch fixed the problem.
I also went in and adjusted the extra ball rewards. Sent test 16 & 17. Awards were for extra balls and that's why I kept getting random extra balls.
Now the game plays great. Only issue is the bottom pop bumper goes off with out a hit every so often randomly. I am wondering if it is the cap on the switch as the gap on the leaf switch does not seem to be causing the issue.
Thank you so much everyone for tips. Thanks again Quench for all the great advice.