Drain tubes are clear. Water appears to be leaking in under the tracks/rails. I found this guide (http://caverpilot.com/cars/how-to-remove-replace-sunroof-in-1991-subaru-legacy-and-stop-leaking-roof-or-headliner/) and proceeded to pull the entire assembly but the tracks appear to be riveted and spot welded to the pan instead of attached with screws like in the writeup. Is this a matter of drilling it all out or should I just silicone around the tracks? Has anyone else dealt with this issue?

I found that making a perimeter seal solved leak. I used 3M rubberized tape , sorry I don't have the product model number.

 

There are only a few sources of sunroof leaks.

 

We were getting just enough leakage to soak the ceiling liner in that area and were also getting damp front carpeting. Inherited this from the previous owner - friends mom - so first thing I did was check the drain holes and read about possible causes.

I will probably do that, with silicone caulk.

 

I think I want to replace the seal around he glass too. Do you know of a source for it?

No , sorry.

Caulk might work if you keep it shut. Using the rubber tape around the rim allows for normal operation. Let us know what you use and how it worked out. Subaru sunroofs are a bit notorious with a little age to them.

bhazard,

 

Another leak source is the plastic drain tubes themselves. Every so often one will split with old age right where they connect to the roof drain channel. I shortened one on my 99 years ago and then put a single loop of mechanics wire around it and twisted it tightly to secure the tube to the drain.