Regarding your trunk fit...take a look underneath and see of the pivot ends of the trunk hinge arms are contacting the underside of the rear deck ahead of the trunk lid and raising it upwards. This was the case on the first cars and although we reported it I don't know if it was addressed. If you find that there is contact just grind down the radius at the end of the arms so that it doesn't protrude beyond the chassis hinge tabs.

Yes, fit the windshield before the doors.

Jeff