They're actually pretty easy to adjust. There are 2 bolts in the bottom of the door that adjust the "tilt" of the window (tilt meaning how far into or away from the rubber molding the glass will come). They can be accessed at any time, as they are always exposed.
With the door panel off, there's a nut towards the front of the door near the top that adjusts the forward/backward movement of the glass. Loosen that one, move the glass fore or aft as desired, then tighten it back up.
With the panel off, there's a bolt, just about dead center of the door that adjusts the "angle" of the window (angle meaning lowering the back but not the front). This bolt is in an oblong hole in the door. Loosen it, and adjust the height of the rear of the glass so that the window will close evenly across the top and re-tihten.
That's it. Just those 3 bolts and 1 nut do all the adjustments you need. Keep in mind that a little adjustment at each point makes a huge difference, so adjust in small increments.