This was all caused by sunroof leak
 

Remember to keep a THICK coat of dielectric grease on the seal! Bummer that you had to go through all that.

they all leak...
 

"a little" is normal and silicone grease helps reduce water intake.the drains can handle normal water but if left open,dust and debris plug drains. i never open unless moving. let it sit ,they will plug up.
73000 on my 10,zero plugged drains.

I think I had the same problem on my Supra. I never leave open while not in truck. Actually I hardly ever open the thing.
Will say, looks brand new inside with the carpet cleaned.