You’re dealing with some of the exact issues I need to deal with on my ‘68 Dart. I guess most old Dart owners have this issue but I’ll be watching real close. Post plenty of pics and good luck.
It will eventually get quarters and a deck filler panel so I'm not shooting for perfection. I'm hoping to make the cut where the vinyl top trim comes across the quarter panel/deck panel. That way the trim hides the weld between the seam.