Start by replacing what are probably the original belts and idler/tensioner pulleys, likely fixing the squeak while you're in there replacing what is probably the front main seal leaking. Sell the cummins and 6r because then you have a real money pit if you attempt that. In all seriousness, why haven't you d-leeted it already? Just run a stock power tune for fuel economy's sake, and enjoy high teens to low 20's empty. From the sale of the cummins and 6r, stick it in a savings account for when your existing motor takes a dump. It's probably due for a set of rocker arms, which is a relatively easy job. They can transfer to your new short block when it goes, unless it goes another 200K miles. It's $5900 for a brand new loaded short block from Ford. Front cover to rear cover; oil pan to oil cooler. If/When it goes, throw a new short block in. It'll come with a fancy parts and labor warranty from FoMoCo that will improve resale value. Perform regular trans service, and it should still have a ton of life left. Throw the emissions crap in your garage in case you decide you want it back to stock to sell it at some point. It's not like programmers lose much resale value. Can't go wrong putting one in.
I always laugh as the fummins guys because after they buy an $8k motor, if they're honest with themselves, they spend a minimum of $5k in conversion parts, an untold amount of time (mostly in wiring), and they still have a bunch of electrical gremlins. Unless they spend another big pile of money, they still don't make as much power as a tuned 6.4, and all they have is a different exhaust note, and a CEL on. Way ahead money-reliability-resale-wise to make what you have work, or drop a new factory short block in if it blows. Then if you stay on top of maintenance, it aught to be good 'til the axle shafts wear out.
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