My sunroof leaked and water would run out of the bottom of the dash and drip on my left foot when driving. I did the same thing "eqs" did with dropping the headliner down a little to inspect the drain tube. When I had a little gap above the headliner I poured an ounce or two of water down the sunroof drain hole and watched to find the leak point. Mine was leaking where the rubber drain tube inserts into tube running down the a pillar. The drain was not plugged because some of the water would drain the whole way through and exit behind the front wheel like its supposed to. "GOPHERIT" is correct, The drain tube in the a pillar is steel and rigidly mounted to the a pillar, (at least at the drain hose coupling interface) but the rubber tube was not inserted very far into it. I pulled one end out and the hose had a crease in it creating an obvious leak path.
I massaged the hose end to make it round again, put some silicone sealant around the outside diameter, and inserted it deeper into the friction fitting. Tested it after the silicone dried by pouring water down the sunroof drain hole again and then put everything back together. I know my condition was not the same as yours but hopefully this helps
2009 GT sport, prem., roof PBM - Red/Onyx
Rotofab, LS7 MAF, Pat G tune, Kooks mids, Mangaflow, 3.45 gears