Diesel fuel is Hydroscopic, that is it absorbs water. Before the last time you run the engine, fill the filter with ATF, then run the engine for about 3 - 4 minutes so the ATF goes thru the IP and injectors, that washes all the diesel fuel out. You can even,(after filling the filter with ATF) put a hose from the lift pump into a quart of ATF. When the engine stops, you know it has run out of ATF as a fuel.
Take the wire off the IP FSS so it can't/won't start.
Drain the oil pan, leave plug out for a day or two, put plug back in, add four quarts (room temp.) of SAE 50W oil, Pull the oil filter, empty it then fill it with 50W, put it back on. Without starting the engine, turn it over with the starter 2 -3 times in 20 second spurts, cool a couple of minutes between starts, that replaces all the old bearing oil, which can be acidic. The old oil left in the oil cooler will replace the fresh oil in the filter.
Drain the coolant, be sure and pull the block drain plugs, one on each side. Remove the t'stat. Plug the radiator hose ports after draining.
IDIoit idea of pulling the heads and doing as he said is good insurance for a long term storage. A little work, but just do it.
***Nothing has to be done to the transmission, just leave the oil in it***
, that is if it's not burnt, but plug/seal the lines that go to a oil cooler. Since your going to scrap the
truck, just cut the lines close to trans, crimp and fold back to seal.