Are both the same year/totally stock shifter? I've heard conflicting reports- some say later year MT82's are better and then there are others saying they're just as bad. I get both the clunk and the notchy 2nd on my 2011 but it's bearable. This is my first stick shift and I assumed it was fairly normal.
Both 2014, same trim build, both Track Pack. The one that does have the clunking is reported as stock by the Ford Dealer that sold the car. That said, it's stockness is dubious to me. It drives very differently from the second one (the smooth one) which I KNOW is stock.
Driving a 2015 GT from the dealer wasn't as smooth and quiet as my Second (smooth shifting) Mustang. It must be an anomaly. Of course my wife wants to switch cars with me, but I won't do that. Hers has the 100,000 mi. Extended warranty, mine only has the standard factory warranty. She needs it more than I since she works and I'm retired.