Will a Shift Kit affect computer commanded controls?

No, it will not.

TransGo Shift Kit® and Reprogramming Kit™ valve body repair kits and  do not make or require any changes to a vehicle’s PCM/TCM programming.

Note: The term ‘reprogramming’ refers to the hydraulic circuit changes that are made with our high performance line of Reprogramming Kit™ valve body kits. The term has no correlation with computer programming.