Hello, just picked up a 85 Gt and have done the rebuilds on the motors as they would just spin the top and would not move the arm. After doing this I put them back in the car and they are acting wired/working sometimes. I know that the actual motors and gears now are fine but I am not sure if it is a problem with the isolation switch or the limit switch in the motor of the driver side. The passenger side works well but the driver side will sometimes go up and other times it takes a whiel for it to move, it was also getting hot before the rebuild and I can now hear it clicking after it gets into the up position. I have tried to find answers on the forum but could use some help. (Also the brushes seemed fine when I took it apart.) Anyways thanks in advance, I will update if I figure something out.

Welcome to the Forum!

There is another thread going right now that would help you out. It has diagnostic questions from Fierofool that would apply to you as well.

Battery Drain

elighm, you might pull the motor and check the limiter switch brushes. Just remove the cover plate and you can see the brushes. No need to remove the limiter switch. Frequently, when putting the motor back together, one of the brushes catches on the armature and breaks off. The motor will run but can't generate enough power to break the pointset at the end of travel.

Another common problem for first-time rebuilders is that they allow the rubber D weather seal at the top of the case to remain outside the case. While you have the motor removed, peek up underneath the knob and see if you can see that rubber seal.

Thank you, Gall757.

They are right, just because you checked the brushes on the limiter switch, it could still be the problem. The brushes fall off. Etc. I am not a wireing wizard. there are other ways to do this (but for me) I take the isolation relay from the headlight I know is good, and put it in place of the one I am suspicious of. Try to raise the headlight again and see what happens. If it goes up it could be a bad isolation relay. Or it could just be a problem with the wire pigtail harness. I had one just had to flip the pigtail open and clean it so it could connect better. When doing a motor rebuild it's generally good to use paper to protect the brushes, then gently remove the paper. Rodney Dickman has new brushes with electrical conductive glue. That's what I'll be trying next. No idea how long or if it will help. But limiter switches with good brushes are getting scarce.
The 87 - 88 headlight motors don't have all these glitches, but you would need to wire in a control modulator (they aren't cheap) to use them. And run a little new wire to use the 87-88 headlight motors. Do able if you can wire and find the parts. But from what I'm told it does solve the problem much more permanently. If the Dickman brushes fail, that's my next plan.
The clicking noise should be the limiter switch trying to turn off and on, (usually) which would mean another check of the brushes or if the copper on the motor somehow got overheated and stripped.
Good Luck