Everyone has their opinions. Here are some of mine.
Spend your money wisely. If you have the ability do the work yourself and you will save a bunch of money.
Exhaust of course.
Intake of course (BHAF is going to be fairly restrictive with the air you are going to want to flow. You can use it though. I have done 545hp on a BHAF)
Do your own custom pump. There is a bunch of reading out there on how too build your own injection pump. You can do afc mods, buy or cut a fuel plate, gov springs, dv's, dv holders, mack rack plug (depending on your pump you may not need it). I bought a pump from a shop and would never do it again.
Turbo or turbos. Sounds to me like you are going to want turbos for your application. There have been plenty of kits for sale out there or build your own.
Injectors. There are a lot of options here. And again used is your friend. You can get some good deals if you watch. A 5x. 014 (same size as DDP4s) set should support what you are wanting.
Head work. O-ring, cummins white stripe 60lb springs, torque down your stock bolts (I don't believe you need studs, you can use them if you feel better about it)
The stock lift pump will support quite a bit of power. You can do a lot of other things other than a full fuel system. For a daily driver I like having the stock pump for its reliabilty.
I agree keep the radiator and such in mind. The supporting cast around the motor will help keep you going.
Cam, intercooler, ported head are all extras IMHO. Needed, I doubt it.
The transmission is where you can spend a lot of money. If you are wanting an auto be ready to shell out the $$$$. A manual will probably be the more economical route, but the clutch can get expensive too.
I believe it comes down to what you are going to use the truck for. If you are just daily driving it is going to be different than someone who is always hooked to a trailer, or someone who is drag racing or sled pulling, etc.
My opinions. I am not one for writing checks for people to work on my truck so I may have a different views than others. Good luck with the build.