There's a few different opinions on here of what makes a bulletproof 6.0L.
Stage 1: Basic budget-level bulletproofing.
-Tear down a complete a EGR bulletproof cooler, or delete it.
-Flush with both Restore and VC-9, and replace with a ELC.
-Replace the Oil Cooler while you're in there, to ensure its clog free.
-Install a Coolant filter, ex. from Dieselsite.com
Stage 2: Next level, a little more expensive.
-SCT fitting replacement (if required)
-Turbo Oil return line upgrade ('03-'05 trucks)
-Change the Oil Cooler to a remote condenser or bumper mount radiator type unit. (Bulletproofdiesel)
*Note: This removes the dependency of the Oil / Coolant heat exchange. This is the single largest reliability upgrade you can make to this truck.
Stage 3: Particularly important for those Modding the 6.0L
-Pull the heads, gaskets and stock head bolts.
-Get the heads machined flat, identify and correct flawed heads.
-Reinstall Heads using Ford OEM or Black Onix Gaskets, and ARP Headstuds.
*Do not reinstall using OEM TTY headbolts.
That's the basic rundown of Bulletproofing your 6.0L, and there's a considerable number of threads here to point ya more specifically in the right direction.
Hope this helps, and let us know how your build goes.