My sunroof won't open/close/re-initialize
 

The roof of my car was covered in ice, and I accidentally hit the sunroof button. Naturally it didn't actually open because the roof was frozen shut, but now it won't open/close properly. I tried the re-initialization procedure as outlined in the FSM, but when the roof tilts up in step 1 the motor just grinds some gears and won't auto close. I have gotten it to go approximately into closed position, but I haven't tried anything further as I don't want to fry the sunroof motor or break anything else.

it might have broken some teeth off the gears. you might have to take it apart and replace the broken gear.

Is just the gear available, or would I have to get the whole motor assembly?

The first thing you should do is check and see if the two screws that hold the motor in place are still there. There is a really good DIY that helped me fix mine. It seriously took about 20 min to do. It looks like it would be hard but if you use the DIY anyone can do it.

I finally took it apart. One of the screws had fallen out, but after replacing all 3 screws the motor still just grinds and won't close the roof properly. When I do get it closed, one side of the glass is higher than the other side, as though the two sides of the glass are out of sync somehow.

Three?! I only remember two that fell out. I thread locked them both so I should be good. Your problem doesn't sound like the motor because mine made a grinding sound too before the screw replacement and it has worked normally and quietly since... You can try a reset on the roof motor? I'm curious so let me know what happens either way.