I have my original trunk lid with a repro quarter, and did what Jerry did but to a much lesser degree. I had to cut the quarter's edge up from the tail panel about 5" up the quarter and take out material (pie shaped sliver) and re-weld as the gap near the tail panel was too tight. By doing this the edge of where it meets the tail panel came into line up perfectly.

I think my vert quarter had more room to get it tighter to the proper gap as I don't have the roof to deal with. It also matters how the outer wheel house was fitted if replaced since that can control the lateral movement on the quarter.

I have a spare original trunk lid that I may not use after all which is very good shape if anyone is interested in it. I bought it thinking I would use it, but it is a later vintage than my January built car. It does not have the tab design for the skin of the lid which was typical of 68 and early 69 built cars.