IIRC, the 4.5 still had the lift pump on the fuel filter. In 05/6 they went in tank. I replaced mine with a FASS last year. The stock pump has a hard time keeping up with fuel requirements in stock form, not to mention small mods. You will notice a miss from time to time if you get on it hard. It is the fuel rail going dry.
As for exhaust, you have 4" from the turbo back. IMHO just straight pipe it and call it a day. Of course that is what I did, but its cheap and easy and, besides your cat, removes the most restrictive part of the exhaust. Yes mandrel bent tubes and stainless is cool, but you should have years of work out of the stock exhaust.
You can always try out a smarty, I do have one and like it. The new one will let you change power levels on the fly.
Nice looking truck. The flat bed is great!