Working on a 69 Bee and the rear window trim holes ended up getting filled and painted, don't ask me why and wish I could have a do over on that mess...
Anyway, from a parts car that happens to be a couple hundred miles away from me now I was able to determine the location around the frame, but didn't measure the distance from either the shelf the window sits on or the outer edge to the roof as to what depth the trim clips should be at.
I'm assuming so they are flush with the roof edge but want verification.

Thanks guys!

Cole

Not sure if you have solved this since your post is a little dated now. I just went through the exact same situation on my Charger. Body shop put on new full quarters with sail panels and fixed the window frame and didn't track where all the clip holes went.

What worked for me was to use a parts car as a guide for the spacing like you did and use the new trim clips as the depth guide. Bottom out the clip in the window well to the edge the window seals against. From there drill the hole at the top of the slot in the trim clip. That gives you a little bit of play to adjust it up from. Then do a dry test fit of the trim without sealant on the glass to set the right depth on the clips. I had my back glass installed today and it worked out pretty well.

Good luck!