So, here's what happened.
Tested again the switches and magnet and OK.
I would get an error at power up but nothing in the test report so didn't know where the error was from. (Had a post about that I started) I had also found the shooter lane switch was disconnected. When connected, the switch would cause the ball eject to fire all the balls out one by one. In switch edge test, with the switch connected, activating it would register itself but I noticed the trough ball stack opto would blink slightly on the matrix. I replaced the diode and removed the spade connector on the shooter lane switch. Tested again and the ball stack did not flicker. Powered up and no error. Good. Started a game and manually rolled the ball around to light lock. Rolled up the left lamp and magnet grabbed it and held for a second and dropped it in like it should. Started multiball and let it drain. Lit lock again and hit right ramp and magnet grabbed. Great.
So it appears the shooter lane switch not working caused the magnet not to kick on in the program. I guess a ball count issue since it never saw it in the lane? All other aspects of the game worked ok so I was focusing on the magnet and switches. Thought I'd switch gears to the other issue and seems to have resolved it at least for a game. Which is better than I had. I'll test more later since I'm technically "working" from home today and I should show some production.
I'll update later. Thanks for the suggestions.