I would set a goal and then you research how to accomplish the goal. These trucks are aftercooled, so after adding some fuel, they will get hot. First upgrade I recommend is installing gauges. EGT/Pyro gauge and boost pressure. Fuel pressure wouldnt hurt either if you plan on bigger injectors or other mods besides just turning up the fuel screws. How are you going to use the truck? Heres my suggestions:
Fun/play
Install gauges
New air filter
Removed baffles/fins in air cleaner housing
turn up pre boost fuel
Adjust rack for full fuel delivery
Install governor springs
That will give you a big increase over stock and see how you like it. Truck will run hot on longer pulls.
If thats not enough, add hx50 or similar sized turbo.
If your planning on working the truck, you need to either keep it stock or install an intercooler with the above list. My truck would get hot towing 20k on a stock truck. The cooler air from an intercooler will help tremendously. You will probably see the MRAP radiator/intercooler and a few stand alone intercoolers.
It all depends on what your looking for and how hard your working the truck. I have the fuel turned up on mine and its a big increase over stock but I do work my truck so I have to be careful. I have to constantly watch my EGT gauge. I want to install an intercooler one day to lower temps.