I too own a 2006 LBZ Crew, 4x4, shortbed, and even though I have more than 200,000 miles on mine, I have never seen the numerous issues you have. Do you know the history of your vehicle ?
I have replaced both half-shafts, both front hubs, the tranny cooler and power steering hoses, and at just under 200K, the front brakes although I could have waited (I got anxious).
Your truck has an engine and tranny rebuild (complete or partial ?), and a paintjob at less than 150,000 miles.
The skeptic in me thinks that you are no less than the 3rd owner, and that at least one of the previous owners did not treat this truck kindly. It appears likely that a previous owner had or anticipated mechanical problems and passed the truck (at a bargain) to the diesel mechanic who did the rebuilding, and if he intended to keep the truck, he changed his mind and flipped it to you.
I don't know if CARFAX would show all of the story, but I would have investigated as much as possible. I look for the ownership periods, particularly how many there have been, how long the 2nd owner back held the title, when the mechanic got the title compared to your purchase, service records, etc.
My condolences on your problems, but this doesn't look like a cheap and easy fix.
Carfax is clean, I am indeed 3rd owner. 2nd owner bought in 2012 and started building from there, until he lost a piston due to cracking he stated. He pulled engine and at same time decided to have trans upgraded as well. Long story short but while drivetrain was out it was towed incorrectly and this caused the hood to fly up and cause damage, which was insured by tow company and repaired and repainted at their expense. I do have a fair amount of service records, but some have been tough for previous owner to acquire, namely dmitri's receipt for the rebuild, even though we have both asked numerous times.
Regardless, I took it upon myself to research the owner and the truck a bit before purchase, and took his word on the truck buying sight unseen. Hopefully I was not taken, but I still have a hopeful good feeling about the truck. I am still in contact with the seller who is providing me further receipts as he finds and retrieves them, and again seems like a good person.
Its a bummer buying a new truck that took a month to negotiate, and not being able to even enjoy it for 5 minutes without worry, but I can't imagine the seller would deliver 5 hours if he was worried the truck had issues.
Buying used is always a gamble, this truck was worth it to me for the extras I can see, the paint, low miles, and overall build. Again I am hopeful, prepared for the worst but hopeful for the best. Just wanted a cool reliable camper puller.
...I should have just engaged in a full mid life crisis and bought the new mid engine vet lol