On my 2008 Chevy Impala LS the moon roof will not close flush. It closes almost all the way but will not do the final flush flat close
Open it up all the way and check thoroughly for foreign objects, especially along the track, whatever part you can see. I would hate to have you have to have to take it apart, last resort.. and probably difficult to re assemble avoid that
After you check for and remove foreign objects, lubricate the tracks and assemblies.
You are on the 'right track' here too...
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