Issues after battery change?

I have a 2016 Limited TRD and needed a new battery. Afterwards, the truck hesitated, surged and acted really strange, like you're fluctuating the gas pedal, under easy acceleration. Took it back and they did all kinds of checks, ended up clearing the electronics by disconnecting the battery cables and touching them together to discharge it all. Hooked it all back up and it was fine for a short time, now back to the same issue. Other than being really annoying... any insight? Appreciate any help and thanks. Really didn't want my first post here to be about a problem with a truck I really like!

 

It is kinda hard to tell the severity of what you are describing, but the short answer is kinda.... When you disconnect the truck from power and then power it back up the everything gets wiped and the truck "relearns" your driving style. For example, if you are super hard on the throttle all the time, the truck will learn and hold gears longer during acceleration and other small tweaks like that. It will normally clear after a week or two. If it is more major or does not clear up, I'm way out of my depth on how to help you.