I have a 99 OBW. The Driver side window had been making a poping sound for a while and then stopped working. Took off the door panel and the window track had unbolted itself from the scissor lift. I reattached the window with no problems. But now when the Window rolls up it tilts inside the car. I have to push on the window to get it outside of the weather strip.

 

I can't figure out how to get the damn thing aligned so that it goes up straight. Any ideas?

Take the door panel back off and make sure that the guides that are mounted on the glass are IN the tracks in the front AND rear of the glass. This is very important and might be causing your problem. These guides help the glass remain stable in/out and up/down.

Keep in mind that these guides (white plastic) are probably the most common problem we see with these frameless window setups. Too much stress and "snap"! It is also possible that the arms on the regulator are bent, but doesn't sound like it.

I have never been inside Subaru Door, but maybe you could bolt the rail that hold's glass to the other side of sissor lift. ( just a thought)

Been there with my 97 OBW while installing tinting. you might want to check the white front guide as suggested and there are two adjustable pushers with kind of felt on the window contact side, on the top of the metal that hold the window against the same ones on the other side of the door touching the glass. The bolts may have come loose and allowed the glass to lean in.