I have a 01 ranger 4.0

I toss a tune on it only modifing the governor and the truck refused to shift into third correct (never did before) i return it to stock and I reset the truck it's fine normal. I really would love to make it run little richer (idles and runs better) but I keep running into the issue with shifting to 3 it hits harder and shifts into 3rd at 21mph never did it before. i never changed a value on the transmission only the motor which doesn't make to much sense on why this is a issue now. But goes away when I turn her back stock tune. SCT X4 7015
(new transmission 15k miles ago)