I just posted kinda on this subject under "The Clunk.........I had". You should read it.
As I'm reading the other posters replies to your questions I want to point out my experience with the Pro Cal tuner. Once removed I noticed better throttle response. My Son told me that the benefit with the tune is only about 3-4 hp and 8-9 pound feet of torque. You could feel the torgue at low end with the tune.
Now regarding a new tune. I have in the past gone with a custom tune from RET on my '06 Supercharged Saleen. Greg does a good job and will get it right if there is a problem free of charge.
My Son has done significant research on canned tunes. He is now convinced that AED is the one. He has emailed Sean ........in Shingle Springs CA who has responded quickly every time. A bit cheaper than the custom tune.
Oh yes, and the clunk. If you get a Pro Cal I can't say you'll get the clunk. I did.
I've heard but can't verify that the Pro Cal can reduce your engine warranty. Look into that. I'm not sure if your computer will tell the dealer that you have uploaded a tune even if you remove it from the car when taken to the dealer.
I've read your 'clunking' thread, and the symptoms you describe could be related to tuning. My previous Mustang, a 2009 Bullitt, would occasionally 'buck' in 1st gear, usually after the initial start of the day, or when the engine had cooled for several hours. Shifting immediately into 2nd always resolved the problem, but if left in 1st, it would definitely 'buck' enough to cause drivetrain 'clunk.' It always resolved itself soon after the engine warmed up to normal operating temperature. So, just a thought...
As for the ProCal tune, it doesn't void the warranty if loaded by a Ford/Lincoln dealer. So, Ford will definitely have a record of the tune! A more sensitive throttle response with the ProCal tune might cause a similar condition as I experienced with the 2009 Bullitt. If so, hopefully it resolves itself as the engine warms up, and can be minimized by using 2nd gear under those conditions. I do think the issue was more pronounced with my Bullitt's 3:73 rear axle ratio, the same as my 2014 GT/CS. I got my ProCal tuner Friday afternoon, and with the holiday, haven't been to the dealer yet. But we shall soon find out how it affects drivability in my new Mustang...