I am happy to report that my Dealer was able to restore climate control functionality and they did it without wiping out cell phone profiles or presets.
The dealer also took care of a couple of maintenance items while they were at it and even comped me a loaner vehicle for the day so it was first class service all the way around.
If you have the CC problem after applying v3.2.2 from the SMR web site take it to your dealer because it can be fixed with an APIM update and the Ford mothership will instruct them on how to do it if they don't know how. If they tell you otherwise find another dealer because they're either lazy or just plain full of crap.
At this point MFT is working fine and has been since with the exception of the CC issue which is now fixed. As the saying goes "if it ain't broke don't fix it", so I am not going to bother with future updates unless there's a compelling reason; at which I'll let the dealer do it during a routine maintenance visit.