Wow.. glad I found this thread. I've been driving Manual Transmissions exclusively for 25 years and have had both the worst (1981 Plymouth Reliant) and best (2008 Mazda Miata) manual transmissions out there. When I test drove the 2011 5.0 with MT82 (multiple times... multiple dealers) I was shocked at how smooth take offs in first were (kudos to clutch) and how crisp the shifter was in all gears (kudos to MT82). I took delivery 9/11/10 with 50 miles on the clock and everyone who drove the car that first week also commented on the clutch/tranny being superb.. the best American manual most had ever driven.
Fast forward a few hundred miles and I came to realize that smooth starts from first were impossible... the clutch seemed very on/off... and worse yet, shifts from 1-2 and 2-3 were usually met with a lot of clunking and light grinding. I brought it in and they acknowledged both symptoms. Last week, they replaced the flywheel and entire clutch assembly. When I picked up the car, the smooth starts from 1st seemed like they returned, but the shifting issues were not fixed. Was told to bring it back and they would drive it to compare to a new one... and would most likely replace the tranny.
My transmission was NEVER clunky when new... very much like my miata...click-click-click into gear. If you're experiencing a clunky transmission, BY ALL MEANS... bring it it. The more of us who complain, the sooner they'll get to the bottom of this..