My truck does a hesitation it feels like if I'm not on it , and just rolling through want to say 2nd to 3rd if I give it more gas seems to go away. Have basically the same mods you have minus the tune but, kind or feels like when you shift into to high of a gear n truck lugs a bit .
I have a 2016 2500 6.0 , dont know if we are experiencing the same thing but going to be bringing it in soon