My level of expertise on that is to start over and do it right. The side windows are going to not fit either.
You can get the roof repainted a lot easier than trimming a windshield or vent window frames and side glass. Have you checked the rear window yet?
Next time, measure everything about 43.5 times and make alignment measurements with marks about 6" apart on the A pillars so you can duplicate the correct dimensions.
I would not even CONSIDER trimming a windshield to "fix" your problem.