I should hopefully be getting a tech to ride along with me today (I had a service adviser ride along the first time but I guess him seeing the problem never did anything). It's 100% there no matter what RPM it's shifting at, it's just easiest to show the issue at the higher RPM's using the paddle sifters so you see what gear it should be in. On one occasion event the shop foreman drove my vehicle around for like 20 miles and still said "nope, nothing is wrong". I know cars have gotten more complicated with all the tech and computers, but it really feels like if the computer doesn't say there is a problem, then according to dealer (Ford certified) techs there is no problem. They lack the ability to troubleshoot problems on their own anymore. You are also dead on about it being lots worse when cold.
I've reset the adaptive learning for the transmissions and also the KAM on my own with no luck. I'm in agreement that it's not software at this point and will be bringing up replacing the transmission to see what they say.