That's gonna be a tough one. Could be pcm. Could be wiring harness. Somebody is gonna have to chase that one. I had something else on my mind with the cluster but it couldn't be that with these trucks.
IIRC there isn't enough room in the 08+ fenders on the front to do cut out flares. I don't think they even make them. If you go back to 99-07 they will work with an 8" lift and clear 40s
Trans is talking a chit. Last time over the pass it didn't like life but drives in town good. I'm not sure on the starting issue. Truck is a buddies. I told him I would look at it but he doesn't have the money to fix it. No bed is on the truck. Welder and box are sold.