Katsarnold,
Unfortunately, there are very few specialists for this CVT unit, as Ford only offered it for 3 years, and did not provide much training for the unit to technicians at dealerships. Having been involved in a few Ford shops, I can tell you that most transmission specialists at the dealerships are less inclined to be very familiar with them.
Couple this with the fact that there are very few units out there in operation, and you have a perfect storm, if you will.
I can tell you that the CVT's are largely trouble free in these vehicles. So that's one point.
Your concern sounds exactly like an electronic throttle body failure. This is extremely common with this vehicle. You will even get the same warning light -- the wrench light -- for this concern. I am unclear as to why a transmission concern was theorized - except that there were probably failure codes in the processor for it. So, my armchair diagnosis may be indeed wrong.
They didn't make YOU pay the $5600, did they?!
Good luck.