This is not an led issue, and it is not led ghosting. It's very common for the game to appear to be ok with regular bulbs then exhibit this problem with leds. The issue is going to be one of several things and it's always hard to track down. Somewhere, electrical current is getting through the lamp matrix where it shouldn't. The following are possibilities you need to investigate:
1) diodes. Diodes are the sole solution to incorrect lamps lighting at the wrong times in your lamp matrix. Prior to leds, I've seen games where a bad diode was replaced and a jumper wire is used. Check for backwards diodes, broken diodes, but the most important one will be a 44 base the diode is touching the base.
2) Check your 44 bases in the lamp matrix. These twist easy over time as they age. The two prongs of the base could be touching on one bulb. Unfortunately, the bulb that is causing a the problems could be working fine and it's tough to troubleshoot.
3) check playfield leds that are wired via signs. Trying to think if lotr has any. I had a two bulb sign with wires in wrong order that caused all this in one game I fixed. The playfield signs usually have diodes elsewhere so it's misleading to rule them out. Incorrect wire order on these can be just like a diode being miswired.
4) Check the board transistors. A flaky or shorted transistor can keep a row or column lit when it shouldn't be.
Your problem is probably one issue that is causing everything to break. But it could be multiple issues. Stern has a fantastic lamp test screen. It is critical to use it. The row and col tests specifically are useful here as is the single lamp test. The numbers you want to use for debug are the lamp matrix numbers (row col) not the ordered lamp number. For example, the first lamp is 11 in the matrix and 1 in the ordered lamp list. 11 is useful 1 is not. Pull out your lamp matrix chart and make a complete pattern analysis. This might help you know where to focus your investigation. Sounds like you've done some of this. Not sure if you have done it thoroughly though.
This is one of the most frustrating and toughest problems to solve in game repair. It usually takes me 2-3 hours to track down and solve these issues. I've had it on over 10 games now and the cause has never been the same
Some of the most memorable causes of this issue I can remember are:
1) Star Trek next generation. Op replaced broken lamp diode with a wire. Owner told me game just didn't work with leds.
2) road show. Shirted row resistor caused the cities to be lit when shouldn't
3) shadow. And this was odd. Flaky power board caused the problem when not enough input voltage. If pin was on its own circuit it was fine when moved to a shared circuit it was not.
4) scarred stiff. Diode touching 44 base.
5) my lord of the rings. 44 lamp base touching a partially exposed wire.