In case anyone cares, here's an update. Chris at Jerry's tore down the tranny and indeed it was a worn synchro that caused the grinding. Apparently the clutch is showing some cracking and ought to be replaced too. The total bill for the work (which includes fixing the water pump, the leakey drivers side door, and broken headlamp) is around $3000!
They ran this by CarMax and apparently they are sending one of their technicians by to check it out and verify that the work is needed.
I hope they don't turn me down because there is no way I am shelling out $3 grand of my own cash when I paid for a 3 year/30,000 mile warranty. Should find out today whether I'm fully covered.
Wish me luck!
