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...

I had the same problem but with my Equinox. I tried what the another thread said to do, and even though it is a different make, it worked perfect. Open the sunroof to the vent position, release the button, and then push it in again for 5 - 10 seconds. The sunroof all of suddenly moved and recalibrated itself to the correct position. It now sits even with the roof and the leak is fixed. If I went to the dealership they would probably charge $200 for a fix that takes less than a minute to do.