To start with you should have the coolant filter in place for about 3-5000mi to help clean the system first to remove the casting sand and any other junk in the system from getting stuck in the oil cooler plus i would never leave water in my system just because of rust. Here is the flush i did, i used 48 gallons of distilled water 1/4 tank of fuel and 12.5hrs of my time but my system is clean when you start you can not stop.
This should be in the driverside block drain to ease the pain in draining and getting burned.
QuickOilDrainValve.com - the best way to change oil
Here is another great cooling flush if you have to back flush.
Flushing and cleaning the 6.0
Restore is for cleaning out any silicate goo. VC-9 is for cleaning out iron and scale. Restore Plus is the same as VC-9 and cheaper.
To flush drain the coolant by removing the lower radiator hose from the radiator, and removing the drain plug from the driver side of the block. There is a drain plug on the passenger side also but you have to remove the starter to get to it. I don't bother with that one.
I also highly recommend you pull the thermostat out on your first drain and put the housing back without the thermostat. It only takes about 10 minutes and will save you 2.5 hrs or so in doing this whole procedure.
Ok now put the lower hose back on and the drain plug back in the block if you removed it. This is the procedure you will use each time to drain the system, except you will not touch the thermostat again until you're finished the whole procedure. Make sure that you set your heater to high while doing this to flush out the heater core as well.
Fill the cooling system with distilled water, start the truck and let the water circulate for 5 minutes. (if you did not remove the thermostat you must run the truck until the thermostat opens + 5 minutes to circulate. This takes 15 to 20 minutes each cycle and is why you should just remove the thermostat) Stop the engine. Drain the system and repeat the flush.
Now add at least 1/2 gallon of Restore and fill with distilled water. I used cardboard in front of the radiator because you have to get to 185* 190* for these products to work. Drive truck or run on high idle for 60-90 minutes just before you get back from your drive remove the cardboard this will help in the cool down same on the Restore+ flush. Drain and flush 3 or 4 times. or tell clean
Add 2qts VC-9 or 1/2gal of Restore Plus, top with distilled water, and drive the truck or run on high idle for 60-90 minutes. Now drain and flush until flush water comes out clear and clean. When you get clean flush water, flush 3 more times using distilled water while draining the block.
After your final distilled water drain it is time to put the thermostat back in take a funnel and dump the ELC coolant down the t/stat hole 3 1/2 gallons or till full to the top of the hole that way you have O air in the block, I recommend you install a new thermostat at this point 3C3Z-8575-AA Thermostat with housing come with new o-ring. They are only $30 or so and it is good maintenance procedure to do so and top off with distilled water. Drive the truck or let run for a while topping off with distilled water. Check the truck over the next few days and top up as required while any air left in the system works its way out useing the 1/2 gallon left over but fill with distilled water that will give you 1 gallon of mix fill ONLY to the add mark this is the new full cald mark. Remember the system hold 7 gallons of coolant by draining the driverside block drain and Radiator you remove adout 3 1/2 gallons of DISTILLED water that is why you only use 3 1/2 gallons of concentrate coolant this gives you a 50/50 mix.
Keep some 50/50 ELC on hand to use to top off the cooling system from here out and you are good to go.
new t/stat from Ford it should all come together (housing-t/stat-o-ring) in a box. The part number is RT-1169
My advice is to get some ph strips from Napa and check the ph level before add ELC coolant because you what a ph level of 7.0 if higher you must keep flushing to get to a neutral balance in the distilled water then you can add coolant, for me it was 6 flushes or 24 gallons of distilled water.
Here is the Restore Product from Cummins dealer
Restore Coolant System Cleaner Gallon, CC2610, Fleetguard Cummins
Cooling system cleaner restore plus, CC2638, Fleetguard Cummins