Door weather-strip should be one of the last things installed on the door. Much easier to make adjustments to the door fit if needed without them on. All the weight of the parts can cause the door to drop a bit.
On the doors, here's how I usually do it:
-All door latch parts, latch, pull mechanism/rod
-Exterior door handle, door lock, I usually leave the door lock knob/grommet off until all fitting is complete (the grommets break easily)
-Window regulator and slide that attaches to inner door, click the window regulator arm/roller into the slide
-Leave off the 2 rubber end dipped J-clips for now
-Rear slide assy, start bolts, but leave them loose, attach the upper stop, leave bolts loose and push the slide as far to the inner part of the door as it will go
-Apply a couple layers of cloth tape to the outside/inside of the upper door opening to protect the paint
-Install the vent frame, use the round holes up top to use for installing the double-studded adjustment bolts, these have to be screwed all the way in. Get the vent frame down into the door, but don't attach any bolts
-Install the plastic rollers in the door glass frame and lube the tracks.
-With a helper, guide in the door glass into the door, moving the vent frame up/back so the glass clears and fits into the channel.
-Click the window regulator arms into the door glass frame, you'll want the window regulator arms to be about 1/2 to 3/4 up so it's easy to click the arms in.
-With the door glass in, attach the glass frame stopper and attach the rest of the bolts to the vent frame. (hopefully you noted the adjustment of the adjusters when removing)
-Install fuzzy strips (roll the window all the way down)
-Install the J clips, the big one is important on a 64.5 as that's the bottom stop of the glass, so you'll want to adjust that so the stainless edge of glass is flush with the
-I usually wait to adjust the door glass until most of the car is assembled, and you'll want all weather-strip/rubber bumpers installed before then.
On the quarter glass, it's straight-forward:
-Install window regulator and all other pieces
-Cover top edge of quarter with cloth tape
-Install the big slide, but don't attach
-Best to do with a helper, guide the quarter glass from the outside of the car onto the large slide
-Attach the metal stops onto the quarter glass frame, they can be a pain
-Click the window regulator onto the plastic slides
-Attach the bolts for the large slide
-Attach fuzzy strip on quarter
-Adjust
