RedStx13

I do not know if this is in the right section but here goes, ive got an 09 platinum with the 5.4l and 3.31 setup. Its only got 41k miles on it. Ive tried programming the truck with bullydog and it set off check engine lights and bullydog had no answer for that. Then i tried installing a superchip programmer and it wouldnt take to the truck after several updates and talking with superchips. Then finally i got an edge tuner installed. But when trying to change tire size or anything for that matter it made my transmission act up and when i had 305's on and set the tire size it was putting my speedometer off by 8+ mph. Then when i uninstalled the tuner and went back to factory tires the truck started having shuttering issues with the transmission and lack of acceleration. When i took it to ford they installed the bumpstop kit to help alleviate the problem, but it hasnt. And ford says theres nothing wrong with it. But when they pulled a carfax on the truck there was a driveline flagged on the report but ford said it was ok. So what do i do? Bc i love my truck and dont want to trade it in. I really want to put a tuner on the truck so i can eventually lift it and put bigger tires on.