With alot of patience, the job can be done. I would do as suggested earlier, buy a Fisher body manual and go from there. There are numerous adjustments that you may have to make. I have been sucessful at adjusting 69 windows in the past.
In case you want to play with the window a little more, here's where you might start.
1. Remove the inner door panel.
2. Loosen the upper window stops (front and back)
3. Loosen the fore and aft stops(allows glass to move forward and back). And loosen the fuzzies at the top of the inside of door.
4. Close door with window down and then roll window up to the closed position.
You may have to physically move the glass around to get it where you want it.
5. Check to see how the fit looks and make sure you don't see any big gaps at the quarter seal and at the top of the glass. Shift the glass around as necessary to make everything look even.
6. With the door still closed and the window up, snug the adjustments and lower the window.
7. From here, I'd reloosen the upper stops on the glass tracks and lower them about an eighth of an inch to allow for play in the window hardware and rollers, otherwise, the glass may raise up too high when you crank it up.
8. There are other adjustments to change the angle at which the glass comes up. If the glass is pushing against the weather strip too hard or not hard enough to seal, these will have to be adjusted as well.
These adjustments as I recall are at the top of the door and consist of the fuzzies which stabilize the glass and the upper hardware mounts which you can either move in or out to adjust the angle of the glass.
I hope this is undestandable. If you want more help, e-mail me. Adjusting the glass can be very frustrating because there are actually a few more adjustments than what I have described. If you have completely removed the window hardware and then replaced it, this won't be easy. Good Luck.