I used the stock harness with Current Performance relay/fuse block. I wired it all up and it works perfectly!
I would have Current Performance do what you want,
www.currentperformance.com
Tuning is the 'easy' part, LOL, I get 14-16MPG from my 6.0/4l80 combo with 3.73s. Runs 8.9s @ 80 on motor and 7.8 @ 88 on a 100 shot. Love the truck!!