I'm new to the stang net and I recently purchased a 2007 GT with the TR 3650 transmission and it grinds going into 2nd gear unless you double clutch it, Is this a throw out bearing issue or just a bad clutch plate or sync problems ?
Still have your grinding troubles? It's likely the synchronizer for that gear. It usually only takes one missed shift at high RPM to make them grind. That was the way with my T5 anyway. I had a shop recommend GM Synchromesh fluid. It worked for me; took the grind in my T5 away. For the price of dumping your old fluid and buying a few quarts of that it's well worth it.
My car has a slight leak at the tailshaft (276,00 miles). If I let it get low it grinds some. Top it off and it is fine. So check fluid or even change the fluid to start with.