Ah ha! 3J4 was not plugged in, that solved the insert issue, and likely other things as well. Now it will start a game, play the lights and sounds, flippers and most other coils work, but still issues.
First, everything but the trough kickout worked and at some point the inserts went out as did the display. Switches stopped working and the game has basically crashed aside from the GI still being on.
Power cycled it and it boots fine, and the kickout even worked. Nice. Plunge a ball, play for a little while. It goes out the left outlane and it crashes again. I don't know if it was the switch or the game trying to fire the coil, but I hit other switches and slings and it seemed fine. So a little progress, and seemingly almost there.
I just walked over to it and the sound is still playing as well. Not sure if that helps at all, but it's a thing.