I've searched and there are lots of threads (some from 20 years ago) about removing the quarter windows, but haven't found any on re-installing them.
Is there any adhesive that's better than others? Is Permatex Glass Weld good enough?
Same question for the primer mentioned in the FSM steps. Is it a primer or a cleaner?
Will the dam need to be replaced or does it usually remain intact upon removal?

 

My guess is that any good brand window sealant will work. Ask a local windshield installer what sealant they use and see if you can get the same. If the dam is still intact upon removal I'd leave it on and reinstall together. Chances are you may not find that part available anymore.
So how are you removing the quarter window? The last one I removed I got lucky as the heat from the sun helped the glass separate from the old sealant. On this other car I'm working on it's stuck on there and won't budge.

 

Windo sealant or Sikaflex works to

 

I'm planning on doing it as shown in the FSM. Drill a tiny hole and saw the sealant off with a steel wire/cable wrapped around 2 screwdrivers. The old posts I found said that way works fairly well.

 

I've removed the quarter glass with the wire and screwdriver method. It was a pain but worked. If I ever do it again, I might try an oscillating tool with a dull blade. My only concern would be scratching the glass.

 

i've used the wire method too, it works. for the top leg, its probably the easiest. it will ruin the rubber dam things, which are superfluous, but also one of the first things i look at to see how well you painted it, lol
that corner where the window meets the quarter panel is kind of tricky/hard to get at

the last window i had done, the guy had a razor blade on a long extension, and that actually looked like it was a good way to go.
something like this

it let him slice the glass out from the inside, no danger to the corners.

and you do want to use the same stuff you'd use for a windshield.