[FD12ME]

Additionally - I notice that the transmission is smoother when the engine is colder (at startup) for first mile or so.

I had this same conclusion...it was pretty smooth and predictable until it hit about 130-140 degrees then started to be rough...this was until I hit about 6800mi, where my shifting has gotten worse. 2 to 3 when cold is like I'm getting rear ended...needless to say, it's in the shop and I'm awaiting the old "nothing wrong, nothing to see here, take your car and go away, maybe they'll be a software update before you sell it in 4 years"