I reinstalled the quarter windows in my 69 Dart and have been trying to align them on and off for days now. I work on them for a couple of hours, get frustrated and quit till the next time I feel like trying again. I must have 10-12 hours of total time in so far on trying to align them and they are both still out of whack. Is there some quick and easy method to doing this? I have to believe they had one when installing them on the assembly line since they didn't have a lot of time in between cars.

I dont think there is anything quick or easy. I spent countless hours on my convertible quarter windows. Having a roof dimension that could be variable, like on a convertible adds more frustration. I had to walk away at some point before I punched something.
All I can say is to make small adjustments to one adjuster at a time, else you get carried away. I did spend a lot less time on the next side, if that is any consolation.

Have you tried to realign the vent wing assembly?

If you use the FSM and adjust the in the order stated it is much easier.

Tried doing it by the book today, step by step. No luck. Windows still don't line up nor go up all the way up to meet the weatherstrip. Also, both of the new ball pivot rollers I bought busted when I tried to roll the windows up after adjusting per the book. $40 down the crapper.

What has been done to the car body? Are you sure you have the correct windows?

I took all of the glass out when I had the car painted. I kept all of the parts for each side separated and tagged so I would be sure they would go back in the way they came out. It is all the original glass and tracks that came on the car and it was all in proper working order when I pulled it. If I would have known reinstalling them would have been this much grief, I would have left them in and masked them off when the car was to be painted.

Are you aligning the quarter windows to the body or to the door glass? Only reason I ask is one of my friends was working on his '67 Galaxie and had a similar problem, he couldn't get the quarter windows aligned with the door glass. After days of fighting it he asked an old body man for help. First thing he did was align the quarter window in the body ignoring the door glass and then aligned the door glass to the quarter window. My friend said it took the guy about 25 minutes per side.

I have been trying to align it with the body. For some reason the glass won't go all the way up to the weatherstrip when I have the window raised all the way up. It stops about 1/8"-1/4" below the weatherstrip. Also, when I roll it down (at least on the passenger side) the window doesn't go all the way down. Still a couple of inches of glass showing with it rolled all the way down.

It almost sounds like the guides are in wrong.

Something is way off, either the guides or the stops. What is the chance you have something swapped side for side?

When I took the window tracks out of the car I kept them separate and tagged for their respective sides.

Does anyone know of a source that sells just the rollers that go on the ball pivot studs? I don't really need another pair of the studs as mine are brand new. Just need to replace the rollers that go on the ball pivots that broke.