Well, guess what, problem SOLVED. Finally.
@jmr061, hero that he continues to be in my automotive life, got me hooked up with Sync 3's latest upgrade to 2.2. Every issue fixed. AppLink? Fixed. USB usage? Completely stable. Everything with AppLink is even faster than when it was fully working to begin with.
So, great shoutout to Ford on this one--for making this far more difficult than it had to be.
I pinged the IVT team on this forum, they didn't have much to offer. Called IVT team on the phone? Not much help there either. Went to my dealer, my technician takes a shot in the dark based on research and experience of others, replaces the hub. That doesn't work.
Could anyone just say, "oh, wait until the next update in a month, you'll be fine?"
Nope. Not a one. So, i'm glad this works again. But it pisses me off that it took this long to get here, nobody could call it out to be a software problem when I asked, nor could anyone say that an update was on the way.
Sorry to be angry, but this ball was dropped so many times by Ford CS it isn't even funny. And it really dampens the entire experience of the car when you're fighting the technology more than you are enjoying it.