My shifter has been clunky since day one as well. I have a piece of what looks like is rubber tape coming from behind the a pillar trim piece. A boost pipe clamp is bad as when I tried to tighten it, it just jumped grooves. I'm taking the car in tomorrow and will address all the problems.
Now at 710 miles
I'll be taking it to suntrup kirkwood
Update: made an appointment for Tuesday. They are going to fix my a pillar, check my shifter linkages- the clunk where ever it may be from-, as well as check for boost leaks. The guy seemed very knowledgeable and is going to get me a rental so they can look at extent of the damage.
Update: here at ford, the guy basically just pulled the piece sticking out of the trim and said, yeah we will fix that for you hah. They are going to listen to shifting and check boost clamps as well. Wish me luck. I hope they don't just tell me everything checked.
Everything was alright, they fixed the trim piece and checked everything. Even rode along and listened to my shifting with me driving. The mechanic said it was normal.