JLP

Both my windows are messed up...

Passenger: Water gets in from rain, its not too bad I'll probaly just get new weather stripping as the seal is not too good...
Drivers: Pretty bad, there is about 3/4 inch between the glass and the seal. Its possible for somebody to stick their fingers through the space its thats bad.

Also, the passenger door, when shut, closes "inwards" and is not flush with the rest of the car. Same thing with the driver door except when shut it sticks out.

I plan on getting new doors down the road, but any ideas whats wrong?

FastElectrics

Assuming that you have not played with the window stops . check your door pins.. are your doors sagging. it's possible that a pin replacement kit from the dealer or good aftermarket source will solve the problem. If that is not the problem, you could re-adjust the window stops . you'd need to remove the interior panel to do that. there are stoppers along the top of the door you'll notice those. but an easy way you tell too if you need to re-adjust those .. at the front of the door. beside the side mirror. the black triangle piece. when the window is all the way up. does the window go all the way up that and leave no space left. if there is more room for the window to go up. then you probably need to adjust the stops. other wise I'm not sure. with out seeing any pictures.