Well, I just came back from the Ford garage. The guy who looked at the car actually went for a ride with me. Of course it wasn't acting up like it had been previously (nothing ever seems to go wrong like it should when I take any of my vehicles into the dealer), but there were mild cases of what I was describing. The mechanic told me that I can expect the transmission to, at times, perform as I described (being jerky on some shifts, etc..), because it was not going to act like a normal automatic transmission.
I came home, pulled the battery and instantly noticed smoother shifting. As kam327 mentioned above, I do believe it IS a software/hardware flaw....and I can't help but think it's all in this "adaptive learning"....because the battery pull clears that out...and that's when my car starts shifting better....until the adaptive learning "learns" again.
I'm still not keeping this car past the 36,000 mile warranty.