I had some holes in the backbox that I had to drill out, I filled them with bondo before I sanded the sides of the backbox. That's all done, I put in all new carriage bolts and nuts.
Fixed one pop bumper, was binding. Seems weaker than the other 2 in the solenoid test after the repair.
Now the upper GI is flashing very rapidly. In test mode lower GI fine, upper flashing (set to level 7). Flashes when not in test mode also. I checked J120 and J121 and both are new and pins properly seated.
I'll dig around under the PF a little, not sure why the upper GI freaked out. Indy is probably sad that the game is nearly done and won't be in the workshop much longer.
Edit: Re-seated all connectors on the main power board, lights work! My pinball life package arrived today, so I am adding the last light up at the top of the PF under the lane guides on the far right.