Alright, I'm going to put this write-up here, in case someone else needs to help with this in the future. Basically, this is a write-up on how to adjust and align the 370z side glass / window assembly. (Look at my first post above for the back-story).
The trick is that you need to first make sure the actual glass is sitting properly in the door, that is to say that it is sitting in such a position where when closed it doesnt leave any gaps, no matter how small, between the glass and the rubber insulation against which it closes at the top.
PART 1.
Assuming you glass has been out of the door, and only in those circumstances; take the inside of the door off, you will see two large black OVAL shaped openings, covered by a tape like seal, just pull those back, until you can see inside the door. (these openings are represented as A and B on the bottom picture bellow). Next, lower the window until you see the glass mounting bolts through the A and B openings (about 2/3 down). Next, loosen (do not take out) the bolts. Once you've done this, you can literally grab the glass with both hands and pull it up, down, and a little to the front/back. At this point, you need to set up the glass in such a way so that when the door closes and the glass is automatically raised ~1/2", there are no gaps. I suggest looking at your other door/glass for comparison. So basically, adjust the glass, lightly tighten the A and B bolts, raise the glass all the way, and see how it fits when the door is closed and the glass auto-raises ~1/2". When all done, tighten the A and B bolts all the way.
CHECK: Check that the glass doesn't "catch" for a second when you open the door, because you have it too high up and the auto-raise/lower feature isn't working fast enough to accommodate you quickly opening the door. If so, I suggest lower the glass overall, a little bit.
Perform the Window Adjustment, instructions can be found all around this site and also somewhere around page 2-41 (from memory) of your manual that came with the car. Basically, turn the car to ON position, close the door, operate the window all the way down, then pull the window all the way up, and keep holding the window switch all the way up while it raises and for 3 seconds after it's all the way up.
PART 2.
Next, look at the adjusting bolts B, C and D (shown on the upper diagram bellow). These adjust the angle of the glass, with respect to the top of the car (roof), by adjusting these, you can make the TOP OF THE GLASS angle more INSIDE the car or more OUTSIDE. The service manual says to start with bolt B and C, and to adjust D last. See top diagram in my first post in this thread for the exact instructions. Basically, just align the glass so that it closes right into the middle of the rubber insulation at the top (again refer to your other door for comparison, just look very carefully, helps if you shine a flashlight right up into the insulation, along the line of the glass, makes things much clearer).
Once you have everything set up, road test it to make sure there's no whistling noise coming from anywhere. Good luck. If anyone needs any more specific directions in the future, just send me a PM.
