Recommended:

Cooling system flush with CLR and distilled water
Refill cooling system with Final Charge ELC and distilled water (50/50 mix)
DFuser coolant filter kit
Motorcraft updated de-gas bottle
Motorcraft updated de-gas bottle cap
Motorcraft thermostat assembly
Fumoto block drain valves
Motorcraft block drain plug o-rings for Fumoto drain valves
IPR Research Gen 2 EGR delete kit
Motorcraft updated oil cooler
ARP head studs
Motorcraft headgaskets

Optional:
Install aftermarket EGR cooler (many different companies)
Install stealth EGR delete (Motorcraft)
BPD billet aluminum water pump
BPD billet aluminum radiator
IPR coolant filtration setup (100% filtration, not bypass)

I chose CLR over VC-9 or Restore or Restore+ simply because it's more readily available, cheaper, and I keep bottles of it at home for different uses (plumbing stuff, clearing clogged heater cores, etc.). I chose Final Charge ELC because it's stocked at O'Reilly Auto Parts and is readily available as well. The DFuser coolant kit was my choice out of all the units out there due to price, including 3 filters, and being easily rebuildable if needed. Some of you may have the updated de-gas bottle and cap. Easy way to tell is if your bottle has a sticker for the levels instead of the markings on the plastic and if your cap has the white sticker compared to being all black. Thermostat is replaced during a flush as it has to be removed anyways. The Fumotos are super handy, but you may have issues with the block drains stripping out and you will need to use o-rings instead of the flat washers they come with. I chose to delete the EGR because we have no emissions testing, plus I like the idea of not needing to worry about the cooler and I chose the IPR setup because it has a one-piece setup instead of the two-piece setup and has no welds to leak and deletes the blue silicone hose. For those of you that have emissions testing you can get an aftermarket EGR cooler that functions better than the factory unit. For those people who have emissions testing that is visual only you can simply weld the ends on your factory cooler and reinstall it for a stealth delete. We all know about the updated oil cooler, ARP head studs, and using OEM headgaskets, no need to go into that. It's been shown that the OEM headgaskets don't have issues if installed correctly whereas the aftermarket options have been having issues even with correct installation.

As far as the optional things - they are not things you should tear apart the engine just to install. More-so they are upgraded parts to replace parts that may eventually fail. The water pump and radiator are not known common failure items whereas everything else I listed is. The 05 and up had an updated water pump and they very rarely fail. If you do need to replace a water pump or radiator though these would be great items to install. I myself do not like the 100% filtration setup, but some do, so it's up to you if you want to do a by-pass filtration or inline.

 

Here's what my list currently looks like:

Perform cooling system pressure test, flush using CLR calcium, lime, and rust remover, and fill using FINAL CHARGE Global Extended Life coolant/antifreeze and Great Value distilled water (50/50) (86,264)
DFuser coolant filter kit (includes hoses, fittings, filters, clamps, hardware, and filter mount) (86,264)
Motorcraft updated de-gas bottle (87,014)
Motorcraft updated de-gas bottle cap (includes seal) (87,014)
Motorcraft thermostat assembly (includes seal and housing) (86,264)
IPR GEN2 EGR cooler delete kit (includes bypass manifold, up pipe, and gaskets) (89,717)