The difference in the HP output is the Injectors, DV's, and tuning. There are some other small differences between the years as well, but don't have much if any effect on HP.
Nothing wrong with a 5" pipe, it's just that people that tow a lot typically appreciate a quiet truck.
As for your parts list.
I'd just straight-pipe the stock 3".
As long as your install it without completely screwing up, I don't see a problem with it.
Good idea if your stock GSK's don't rev past 2700.
60# valve springs
Needed if you plan on an exhaust brake, or pulling past 3000 RPM.
This one's up to you, but with your goals in mind, it's likely not needed.
There are alternatives such as just retorquing the stockers or SHCS, but whatever floats your goat.
South bend clutch
I've had good luck with valair as well, but that's up to you. Which clutch were you planning on?
O-ring the head while it is off??
Why is it coming off? The stock gasket with a little help can hold some decent power, once you need to replace the gasket, a little port work and O-rings may be a good idea.
Stocker should do you fine.
I wouldn't bother.
Tranny input shaft??
The clutch you get may decide that, but if you wanna keep your options open for compounds, it's probably a good idea.
Like mentioned, you'll need to do something about your lift pump.
Stock hx35 + ht3b
I'd hold off on the compounds at first, you may decide you don't need them. A lot of people underestimate exactly how much pull the stocker is capable of. It's also a good idea to play with tuning and get a feel for it before throwing another turbo into the mix.
Yes and lots of it.
#10 fuel plate
Like say, I'd do either the AFC stop bolt mod, or a #100 plate.
Please read up on injectors, the "XXHP Injectors" terminology is misleading, and it's only purpose is to sell low quality injectors to unsuspecting people who just want HP. You wanna get the real deal? Pick the ones you want by hole count and size. In your case, a 90hp injector is around a 5x12, which is a good size for your build, but if you know you'll be doing compounds and you wanna get everything you can out of them, then you may want to upsize them to a 5x13 or 5x14.
Timing 15-16° btdc
You used the '°' symbol....
Yes Tony, I stole it. And yeah 15-16° is a good starting point.