It's funny: I always wondered what that one tool in the kit was for. Haha!
Anyway, this morning with a little more time on my hands and my buddy helping me eye it out, I fixed it and everything is working fine. Took the rear drain channel off, which without the glass on is the only thing connecting the two glass brackets. Doing that freed them up somehow, but they still weren't even. It took some finesse, holding one still while operating the motor to line them up. Once we thought we had 'em good and lined up we sent them to the full closed position, put the glass back in, made sure everything sealed up and called it fixed.
The problem basically was that without the glass connecting them the 2 glass brackets are able to move independently of each other (to an extent) and the passenger side on mine doesn't seem to move as smoothly as the driver side. Thats how it wound up getting stuck and uneven and giving me grief. Gonna try the DIY tomorrow with the glass in, I saw somewhere on here that a few have done that.
Any tips on that?