Window dropping as if top is about to go up/down
 

I can't seem to find anyone reporting the same issue that I'm having, though I admit that I'm having trouble figuring out exactly what search terms to use. I replaced the driver's side window regulator. Everything there seemed to go fine, so I moved on to making height adjustments. I thought I had it nailed, but now when the window goes all the way up, it drops the 4-5" that it would drop if I was about to put the top up/down. The top is fully up and the latch fully engaged, and the passenger side window is not moving. Any ideas? I'm asking before making any further adjustments, because the window height looks correct, both at the front side of the window and the back side. I've held down the window button to train it on previous adjustments, but then found that it should move a little.

If it is going down the same as if the top was opening, it may be a problem with the top latch microswitch. Open the latch for the top and poke something in where the little hook latches. Push it in all the way and hold it while putting the window all the way up. Does that change the operation of the window?

That did not change the window operation. I did hear the microswitch "switch". Also tried the passenger window and it went all the way up and stayed up.

My situation: with top up (closed), windows would drop about 3 inches and not go up. Could lower windows but going up they stop at 3 inches. Replaced the micro switch at the latch, no change. Pulled the relay and everything is fine. I have previously changed to manual top operation.

Sounds like you've covered a lot of the common issues. Since replacing the micro switch and pulling the relay didn't help, you might want to check the window motor or its connections. Sometimes, manual top operation changes can affect window operation. Also, inspect for any binding or obstructions in the window tracks. Hope this helps!