Ok, you seem to have a couple of different issues.
LED L17 is associated with F5 : 7A 250V SLO-BLO, is the 48VAC feed to BRDG 1 / 50VDC Coils / Flippers.
If your front door interlock is in the 'let's power the flippers' position, this LED should be on, so don't panic.
Any time I've got a flipper on a stern with a normally closed End of Stroke, I put an alligator clip across the two End of Stroke terminals to test it. The End of Stroke switch has to make INSANELY tight connection, I mean really pinch those contacts together or you end up with dead flipper (This was worse in Jurassic Park Data East days). I short out the End of Stroke to make sure that it isn't causing the flipper problem and test it. If it works with the EOS switch shorted closed with the alligator clip, but doesn't when you remove the alligator clip, replace the EOS switch. Don't examine it, don't adjust it, replace it.
However, you've got a slowly raising flipper! I would carefully examine the previous work replacing Q16. If the board is carbonized (browned, blackened), you could have trace voltages causing problems, but I suspect that a VERY careful examination of that whole section will reveal something not connected. Also, clean your flux. I haven't had real problems with flux residue, but you could have some trace voltage activating the gate of that IRL540 mosfet. Getting that circuit board repair perfect is a very good step.
If the flipper wasn't raising by itself, I'd suggest taking an alligator clip and grounding the tab of Q16. This verifies that the board is capable of activating the flipper coil (the flipper coil is properly connected to power on one side, and to the Mosfet on the circuit board). If you can activate the coil with an alligator clip you then know it's something not activating Q16, not something that is a problem between Q16 and the coil.
You should be reading the 50V (might be 78v measured) on basically all terminals of all the flippers when in game mode or coil test mode. Measure the voltage to the terminals on the right flipper and see if there is something different than the terminals on the left flipper. Let us know what you find.
You are also having problems with the portal bank motor starting when you have 50V to the flipper fuse installed.
Weird.
Is this just a 'Oh, I have a problem with the switch that is telling me that the 3-bank is up or down so I'm running the motor'? From the tone of your post, I'm going to suggest some things that might be a lot more strange than that.
Q6 is what activates the relay to activate the motor. I am always suspect of relay board solder connections, so go ahead and resolder everything on the bottom of the Relay board. This won't fix anything, but it'll make you feel better. Hehe.
On power up, hold your finger on the relay. Can you hear it clicking to enable power to the motor? This will point you to whether it's a relay activated all the time problem or something completely strange with the AC voltage to the motor.
Is there a shorted wire somehow making connection between the AC for the motor (16v AC) and the flipper wires? I don't think so because I don't think that the two problems are related. There is a Yel-Blk wire and a Blk-Orn wire associated with the 16v power to the motor (if I'm reading the manual correctly, one of the problems with Tron is they made four different versions!). If that motor is turning by itself it has to be getting power either through the relay contacts, or because something is touching inappropriately.
Let us know what you find. Pinball repair can be hard, and you've got some really unusual things going on here. Keep plugging away at it, and I'm sure you can get it fixed.