The dealership gave me a call tonight saying the car was done and good to go! The gasket around the input shaft was improperly installed at the factory. I've already picked it up and it's driving great. Third gear is easier to engage with no grinding and the clutch feels great.
As a bonus, they installed my AWR Front Motor Mount without me asking. I figured they wouldn't do it so I didn't bring it up. It's the 70 Durometer, and it feels FANTASTIC! Before I could feel the engine/tranny moving around as I shifted. Now it doesn't move at all, a major improvement. There are some vibrations at idle, but it seemed to smooth out as I drove. We'll see how it breaks in.