[Blas]

The back side of the hardtop could be pulled too close to the body with the two latches near the doors. The hardtops rear rubber seal should just lightly rest against the body which also minimizes the scraching of the paint. If the rubber seal is compressed, then it's way too snug back there. Correcting this by slightly raising the hard top in the rear should give you a little more room at the doors for the side curtains.
Were the top and sidecurtains on the car when you got it? I'll bet the sidecurtains were in the trunk right?
Are the hardtop latches near the door tops straight or cocked at an angle?
I ask because if the windshield was replaced, the windshields angle might not be correct (ie. diferent from when the hardtop was first installed) making the top of the windshield frame lower in front, which would add to the fit-up problems with the side curtain too.
There are a few other things you should look into on the chassis too.
You can contact me directly with any other questions if you like...