You're problem with the sunroof seems to happen quite a bit over time... Usually see more seal problems with aftermarket sunroofs, but I don't trust the OEM factory ones much over time either. Nice to see you investigated and found the issues so far. I like the needle-nose shop vac btw... lol.

On the same topic, you might want to pick up a can of spray-silicone and hose the weatherstripping down a bit... it cleans it and keeps the rubber nourished (prevents cracking/leaking).