[Kube]

Mike, I'd restored enough of these cars to appreciate your frustration.
The issue you deem a common problem is more often than not due to poor restoration techniques and less of a factory assembly issue.
Every one that I have restored has had at least some moments of ARGGGHHH! when attempting to fit the windows / top assembly.
I have never had the need to remove a regulator stop.
However, I have had to adjust the top, adjust the window regulator & tracks, repeat, repeat and repeat. I doo all of this prior to committing to the top placement. IE prior to tacking permanently in place.
Lots of patience required.
If your top is old and has shrunk, there is a chance you will never achieve the desired result. If the top was not installed properly, again, you will most likely not achieve the desired result.