I sealed up the moon roofs with chimney sealant some time ago and they are watertight. After a big rain I will get water coming down by the front doors just behind the headliner. After looking things over it appears that water must be getting in on top of the front a-pillars where the drip rail ends.

I assume the best way to fix this is to smear some sealant around this area. Has anybody else dealt with this?

 

Did you seal around the outer plastic part of the sunroof, not just around the glass? That's where the water gets in and it will leak into and out of the catch tray, into the headliner, and out the edges around the tops of the doors. The best way to seal the sunroof is to remove the headliner, remove/clean/seal the sunroof assembly, reinstall everything. ..But it's a lot of work.