I used the trans am pan. I haven't read all the Pirate stuff but I have not had a problem other than losing oil pressure when I flop (DUH) or am straight up on a climb I don't belong on. I run 6 quarts of oil.
I never even considered headers. There is enough heat in the engine bay without headers adding to it. My philosophy was to keep it as close to stock as possible....... I don't need problems out in the trails. We tried a variety of exhaust manifolds, forward facing, etc and ended up using the stock truck manifolds that came with it. (mine is an 03 Escalade installed in a yj)
I also had Jim's performance do mine. Zero issues with it right from the get go. I sent him the harness & ECM. He pulled all the unnecessary wires and everything came back clearly labeled. Was literally plug & play. I wouldn't argue with the dyno tune advice but I'm not sure how much you really need it. The stock 6.0 gives plenty of umph. I have no idea what my HP is over the factory 345 HP. Jim @ Jim's Performance told me that with the minor changes that I could consider I might have another 25 HP but no guarantees. So, I'm definitely south of 400 HP and don't see the need for more. Have there been a couple times where I felt it could use more? Naturally. It's also not a drag jeep so it's fast for a jeep but not fast for a drag jeep. It's good as an all around hill climber and trail rig.
Don't waste your time with fuel delivery. Use a 60 psi minimum in-tank fuel pump & a factory pressure regulator.
I would assume yours is a drive by wire. Make sure you have the EXACT match pedal & module from the donor truck. Just because they plug in doesn't mean they are compatible. (ask me how I know
I left my intake forward facing. Personal preference IMO, whatever works.
Good luck with it.