What do you mean by out of alignment...? As far as the bolt locations, definetly see Legendtuner.com, but if you can describe your problem I might be able to give you a quick rundown of whats wrong internally...
I have had about every problem with my window that you could hope (NOT) to have... My window guide rail was bent, my window seal was torn and created wind noise, at one point when you rolled up my window you could stick your fingers out!
If the part of the window near the door seal is "popping" up out of the glass run channel, chances are you just need to pop off the door panel and unhook all the wiring, then take a socket and loosen the only screw that has a "slot" for adjustment, and try bottoming it out in the slot. If this bolt is set too high, it can cause this problem.
