I think that the key here is that the OP has said he has lost confidence in his truck. Will he ever trust it again, hard to say but not real likely. We faced the same general dilemma last spring with our 2002 Dodge Cummins with 144,000 miles on it. Not any real problems but overall it needed about $10,000 to be spent on it to keep. i.e. new paint, new interior, tranny rebuild, add an exhaust brake, etc. or trade it. So we traded it for the current Chevy. Wanted to find another Dodge but couldn't find a one ton DRW diesel crew cab that was pimped out like I wanted one. So the Chevy dealer got the sale.
I have a rule of thumb that when a vehicle needs repairs in the amount that it is worth for a trade in, it is time to sell or trade. My Dodge needed $10K in work and was worth about $10K.
The people with the 6.0 Ford that go through a full bullet proofing job, at about $4,500 seem to be very satisfied with the results. There is nothing basically wrong with the 6.0, other than Ford messed up on the EGR cooler, the sand in the block casting, needing a coolant filter, and replacing the head bolts. If I owned a 6.0 that I liked, except for the original built in problems, I would probably go for the $4,500 engine improvement. Getting those items replaced with after market would more than likely give the OP several hundred thousand miles of service with his truck. None of us have any guarantees that our truck won't break down today or tomorrow.