You deserve credit for finishing the difficult kit.
Next time, spend extra time on dry fit. It's a standard procedure during preparation of any kit from old to new. Today's CAD-designed kits have extremely small tolerance, and deformation of plastic at the time of removal from the mold is very difficult to predict.
Most of the manufacturers (except for Tamiya and Bandai) don't spend extra time on correcting the mold by hand (and experienced mold masters are getting fewer), so some of the perfectly designed parts (on the computer) can have a bad fitment issue.
Dry fit should help you identify poor-fitting parts before painting, so the overall build quality will be better.