I saw the PM that you sent me today about this issue, jwoolsey08. I'm replying here so others can see my response too.
I never did install a new shifter, and I'm still experiencing the issue with this car.
At my next scheduled maintenance after I had posted above that the dealership service advisor told me that he could find no technical bulletin on this issue for my VIN, I had a mechanic ride with me while I shifted from 1st to 2nd a few times. He heard the clunk, but all he could say about it is "that's completely normal."
I find that I can minimize the clunk if I don't pull so hard when shifting from 1st to 2nd, and if I push the shifter a bit to the left as I pull it down. It bugs the hell out of me that I should have to do that though.
At some point before my warranty expires, I'll ask another mechanic to check it out.
2014 Mustang GT Premium
5.0L V8, 6-speed manual, 3.73 axle
Mods listed in profile.
Ordered 2 June 2013 | Delivered 15 August 2013.