I think I have it figured out. If I start and stop the car after putting in a new tune, and then start driving the transmission shifting hesitation almost nearly completely goes away. It is similar to how my DHP performed on my 97 years ago (if I wrote in a new tune, and start the car the first time ALL trouble codes would show and the transmission would not command gears on time).

Are there any parameters that are not available to HPT for the transmission? It feels like the more I drive it the more the shift points and timing are correct, as if it is learning.