I remember the door channels along the sides of my windshield frame being damaged by the Previous Owner (PO) who didn't seem to mind where he was mounting the metal top. Those large metal screws were not spaced evenly nor in a straight line. Some went right through the door channel. I bent it back to near straight with a screwdriver and then convinced the body shop in Kansas to weld the hole up but leave the channel as is (I seem to recall cutting a brass bar to a small square rod so he would have something inside the channel when welding) but I don't think he used it.
Later I took a Dremel to it (threaded the bit down the channel to the weld spot where the build up was). And turned it on. Carefully, I ground the weld build up on the back side down to where I was able to test fit my old door to see if it would slide.
Another hobby that I've spent a lot of time in - we would often find ourselves making tools where one didn't exist. Not seeing what this channel looks like, I wonder if a small insert wrapped in fine sand paper, complete with a 90 degree handle to hold on to, couldn't be slid around the perimeter to see if there's build up (paint/crude/etc.) somewhere as well as add a slight polish to the inner surface. I'm not sure a power tool would be a good idea in this case.
Heck, you might even get it to cooperate with an aggressive scrub using an old toothbrush!
Let us know what you find!
'54 CJ-3B "Green Gruntt"