I have a 91 Accord EX. I opened the roof and when I went to close it, it did not fully finish. Very small ~1/2" distance, but you can see the back of the roof has not fully lifted. It worked fine for years, and then all of a sudden this happened...I looked for debris or other obvious things in the track, but I don't see anything. I tried the manual nut under the plug in the headliner, but it still won't close. Any ideas? Thanks much!

 

Could possibly just need to be greased. Mine didn't open all the way until I greased it. It could also be the start of a bad motor. Anyway, try properly greasing it, and see if that does any good.

 

Check the are where the glass slides on. On my accord there was a metal piece that became loose and it stuck out, preventing the glass from closing all the way. Its held by a single screw.

Maybe that'll help.