A couple of things,
1. Deck lid lines up great in the rear and flush with the quarters. the front though is off, i dont have exact measurements but by eyeballing it its way off. what is the best way to get the same gap? i did not replace the full quarters (just the lower).
2. The weather seal (new) lands directly in the inside rail (rain channel rail) is this correct?

Thanks

 

move in very, very small increments. a 1/32 makes a big difference. I suggest working on one hinge at a time, and keeping the nuts snug. find a spot next to the hinge and use it as a reference, or even use a piece of tape. sounds like you're already in place, just need to move it back a little.

 

I have the same problem with my 68 coupe. To get the gap on the hinge end correct, the rear does not line up with the quarter panel extensions. In my case, it's short by about 1/2". I assume it's the replacement trunk lid and I'm going to measure it against the original rusted one. I've been busy with other work on the car and put this problem off. I've found that some reproduction parts (like the replacement rear valance) are not very precise in their measurements.