Thinking back on it I believe my order on my 68's has been
1. vent window and frame, install loose, tilt forward a bit.
2. scissor mechanism
3. rear guide
4. track on rollers
5. glass in, attach to track
6. install stops
7. initial adjustment, vent frame to body, then rear guide, then stops
8. window felts
9. lower bumpers
Will be doing it on the GTCS soon, in the next few weeks, so post any tips!
I'll be striping the scoops before window installation, so a slightly different order as no holes are in the rear 1/4 side plates.
I do have a write up on rear 1/4 window install, PM me an email address if you would like a copy....