Fellow E99 guy, E99 being what it is, you've got your work cut out for you. E99 specific turbos and support parts like bellowed up pipes make the L99 or T4 conversion economical for us. If you can swing the conversion to L99 parts, the latest KC38R 366 looks to be where it's at for a stock appearance bolt on tow turbo, if you're in a non-emissions area, a T4 swap and S666SXE is what the latest KC unit is based off of. The stock HPOP on our trucks is lower volume so it can't maintain pressure as well. That means a pump change or careful injector choice. I've seen a lot of guys swear by 238/100s, making them a definite possibility to me, I'm personally torn between the simplicity of 160/30s and performance potential of 200/80s, with the 200/80s taking less oil than the stock ABs and a seemingly perfect match for the latest KC38R 366, this is the setup I'm looking to replace my D66 and AB codes with. You'll want to update to a later PCM from a 2000-2001 to make tuning easier.
Now, if you really want the truck to be a whole lot better, you'll do what I did and rip the E99 axles, steering, suspension, and brakes out from under the truck and swap it over to '05+ steering, suspension, axles, brakes, wheels and tires. You can find 4.10 and 4.30 geared axles that will make better use of the power and put less strain on the engine, clutch, transmission and everything else. The biggest benefits are turning radius, stopping distance, ride quality, and most importantly, component life, the newer stuff is just simply superior in almost every way, and as an added bonus, the truck sits as high as a leveled leaf spring truck from the coil swap making 33-35" tire fitment a breeze.
I had the ZF6 and a South Bend single behind my 6.0L, I miss having the manual at times, other times, I just wish we had a more modern 6-spd auto behind the 7.3L in place of the outdated 4R100.