xkbx

A little backround, 08' F150, 5.4V8. 35'' nitto trail grapplers. k&n intake. I got some good info from some guys on here a few months ago when I sunk my truck in about 5 feet of water. Transmission was real bad. I flushed it twice, got the fluid the right color again. Checked the differentials and there wasn't any water in them. Changed the engine oil. Problem is the transmission still like, chirps, when im going from neutral to 1-2. It feels a tiny bit rough but the squeek is definitely noticeable. Ive been reading around and some people that have had their tranny chirp were talking about shift pressure being off cause of the bigger tires and im not sure if thats a possibility with mine. Im obviously inclined to think there is still something messed up due to the water, maybe something in the linkages? Thoughts?
Thanks in advance