Is there any battery damage on the MPU?

Were those things working before you did the work to it?

Its been my experience that flaky power ups (which can result in locked on coils and lights) can be due to either a bad power supply (has nothing to do with if voltages are present or not, it has to due with how fast each of the voltages come up upon applying power) or a bad MPU board. Unfortunately, the best way to determine the problem is to test either part in a known good game.

There is a modification I do to the Sys 1 Driver boards to prevent that power up clunk that games do if they have coils being driven by lamp circuits (similar to John Robertson's System 80 mod). It resets all the latches upon power up so in case the MPU does not wake up properly and clear all the latches, they are already cleared. Most solenoids are directly driven by the MPU Spider chips (no latches involved) so this only applies to game that use a Lamp driver, to drive another transistor on the playfield (such as Joker Poker etc.).

Depending on how much you mean that the outlanes cause the Display's to flicker: It is normal for the CPU to pause each time a switch closure is made on the playfield, this results in a little bit of flicker somewhere in one or all of the displays. The CPU is rather slow, so when it sees a switch closure, it has to go off and service it and this can result in a brief "hick-up" in it servicing the display matrix. But it is only for a brief moment. If your displays are "Fluttering" like they would if you hit the slam switch, then there is something else going on.

Do see if you can beg/borrow a KNOWN working power supply, or a known working machine you can drop it into for testing. Power supply voltage issues can cause all sorts of oddball behaviors in an otherwise working MPU. Our own Solar Ride, for instance, was doing all sorts of bonus/drop target counting for switches not being physically hit, in fact I saw switches come up on the switch test that DON'T EVEN PHYSICALLY EXIST IN THE MATRIX, and eventually it just started to lock up until it would warm up. I finally bit the bullet and ordered a completely brand new power supply from Marco rather than attempt a rebuild (I already have one "carcass" from an attempted rebuild on a supply that was marginal, and didn't want to fiddle with doing it again), and it cleared the problem right up.

And yes, even while it's sitting idle, not in a game, the displays do flicker slightly when you press a switch. It's normal for any System 1 to do that.