So I guess I gloated a bit too quickly in my last post: while I had gotten through the final repair, a new thing cropped up:
When the lights stopped rotating for the skill shot and settled on a hole, the right most rollover would be triggered with a DING and of course that means the ball save timer has started.
I assumed that while the playfield was up and I was swapping LEDs that I had bumped the switch and it was closed always. Checked the switch and the gapping was fine.
So what was different? I noticed the wire bundle going to the lights was touching the wire from the switch.
They weren't shorting, the wires were all insulated, but I imagine the wire used for the lower-power switches is less insulated, and having the light wires up against it caused some leakage and a false positive.
I bent/redirected the wires away from each other and voila, the problem went away.