OK, this is kinda complicated, so put your reading glasses on, and put down the beer.
There are five major items you can adjust that control the movement and placement of the window. If you have a hard time finding some of them, watch the tracks move while rolling the window up and down a few times.
The front stop that controls how high the window goes. There are two bolts on this one. It governs the FINAL height of the front of the window, when it is all the way up. The heads of the bolts face IN.
The back stop that controls how high the window goes. One bolt. It governs the FINAL height of the back of the window, when it is all the way up. The head of the bolt faces IN.
The side stops (along the top, there's two of them) that push/pull the window in or out when it's all the way up. They have one bolt each. The heads of the bolts face UP.
The rearward end of the short horizontal end of a track, it controls if the window is higher in the front than in the back or vice versa when partly open. Remember that #1 and #2 just adjust the final position, this one adjusts the position when partly open and when in motion. To find this one, look down into the door. About in the middle, there is a short (8 inch?) horizontal piece of track. It's fastened at both ends by a bolt (one at each end, heads face IN) the rearward end has a slot so you can loosen the bolt and adjust up or down. I'd recommend loosening the right bolt as it makes sliding the left one up or down much easier.
The top end of the vertical track can move in and out, if you move it more OUT, the window moves IN because it's on the other side of the lever (the window) from the fulcrum (the top edge of the door). To find this one, roll the window down all the way and look down from the top. About 2/3 or 3/4 of the way to the rear there is one vertical track. There is only one vertical track anywhere in there. About four inches from the top of it is a mounting point. The mounting thing is a horizontal piece of metal about 4 or 5 inches wide, sticks out about 2 inches. There are two bolts in it, the heads face DOWN. Since you're looking down from above, you'll see the ends of the bolts.
Adjusting #5 is the hardest so I'll describe that first.
Loosen the two bolts. You'll probably have to loosen them a LOT to get the track to move, and jiggle it a lot. DON'T remove the bolts though! The washers on them have metal spikes on the face so they act like lockwashers, also means they don't slide real easy. But the track is under a little tension (I assume from the weight of the glass) and I doubt you'd ever get it to line up again if you remove the bolts all the way.
Anyway, these two bolts allow the mounting point to slide IN and OUT. Keep in mind that this adjustment moves the window in the opposite direction (moving the mounting points OUT moves the window IN). Adjustments should always be small, the window is very large compared to the track so a small change in the track location moves the window quite a bit.
#1, #2, #3, and #4 are fairly straightforward to adjust. However I would recommend adjusting #4 and #5 first, and every time you make an adjustment roll the window up and down a couple times to make sure you like the way it looks when in motion.
When adjusting #3 and #5, put the interior panel back before test-rolling the window up and down (you don't need to put the armrest and trim back). This is because the pressure of the panel against the glass alters how the glass is angled. I had to find this out the hard way... thought I had it working perfect, reassembled everything, it was screwed up. This is even more important when adjusting #3 since those only control the fully closed position of the glass.
#1, #2, and #4 can be adjusted without putting the interior panel back, since they only control the front/rear angle of the glass, not the in/out angle.
The #3's should not press against the glass when it is moving. This can cause the motor (or your arm) undue strain.
What to look for:
The glass should move smoothly up and down, it shouldn't change angle (either front/back or in/out) sharply when it hits the final stops.
When the door is open slightly (an inch) the glass should be parallel to the weatherstripping, it shouldn't touch the rubber before the door is closed, and it shouldn't angle out from the rubber with the door fully closed. Check this at several points of the window's travel... I.E. with the window 3 inches up, 6 inches up, 9 inches up, fully up.
The door shouldn't rattle excessively. For whatever reason, when my window was maladjusted the door rattled more than normal. When I adjusted it correctly, the rattles quieted a lot. There are other things that can make the door rattle but maladjusted windows will do it too.
The windows shouldn't leak excessively. Obviously this depends on the condition of the weather stripping as well as the adjustment of t-tops (if you have them) but if too much air leaks, try angling the glass to press in slightly (#3 and #5) or if it leaks more from the rear or the front, angle the glass slightly to the rear or the front (#1,#2,#4).