Wheels: i have always liked mickey thompson classic 2, and dick cepek dc7, 20's have some weight drawbacks, whatever size rim dia you choose, go 9.5-10" wide, run a 5-5 3/4" bs and a 305/50/20:thumb: i would probably run mickey thompson tires too
Stereo stuff sounds like you got covered, but i would run a single twelve , and do a complete separate staged mid an hi in the door and pillar, some thing like 61/2" mid, and a 3" and tweet, i would run an alpine digital 5 channel amp as an all in one, or the 4 channel with a dedicated mono sub amp
Obviously deck choice is very personal, kinda like rims, double din, alpine, pioneer and jvc have some killer decks out, as long as your spending a cool G on a deck your good there.
At 5-600whp i think you're safe to run the egr, and nithing is as cost effective or as simple as a stg 2 garrett 4094 avan turbo upgrade, its not as bad as some have made it out to be, i like it and have not come close to tapping it out, or even dialing it in all the way.
All season big air kit with grid and egr delete is what i would do, if i were to do it again, and I'd also do the y-bridge, i know, i know, most will say b.s, and i have not driven my truck with it yet, but i have some high expectations for the bridge, when taken into account the other flow mods i have, and the crude and poor, poor design of the factory piece was revealed to me.