both my driver and passenger side windows dont line up correctly. the pass. side doesnt even roll all the way up to the weatherstripping (maybe about 1/4 to 1/2 inch away) and the drivers side seems to be too high in the back (hits the weatherstripping and pushes outward) how the heck do i adjust these things?

 

(i posted this same issue not too long ago) i had your exact problem after installing a new door and quarter panel (actually that entire side due to an accident). i fixed mine by looking for all adjustments in all windows (in nooks and crannys) and even just loosening everything and repositioning it all. can't say much but take all the panels off and end rubber seals to get to see the adjustments and take a day to look/find the adjustments and mess with them. if it is already off adjustment, how much worse can it get? mine aren't even perfect, i just found a medium happy and left it at that. sometimes with my case aftermarket parts don't always work so perfectly. they are always off in something. it is hard though, just mess with it long enough and you'll get it.

 

+1 it takes some time if your not doing it everyday , like above look for all adjustments and move them a little at a time . As for the not going up all the way regulator may be worn and jumped a tooth roll it up and look at it . Make sure it didn't run into a obstruction .