Exact same issues Bro
Your F350's symptoms are identical to my 2004 F250. My truck is currently at the ford service department with the cab off getting new head gaskets and an EGR cooler. It is about a week long repair they tell me (with their schedule). I would be very careful if you are still driving the truck because to problem will get perpetually worse. It starts out smoking like a mother, which is probably burning coolant from the leaking gaskets and the heat of the failing EGR cooler. Watch your coolant levels closely because your temp gauge will go from what seems to be ok to "OH MY GOD" in seconds. And even though the 6.0 has some fail safes, heat is a killer. As far as I know you should still be under warranty until 100k miles.
I absolutely agree that you should find another place for service. Start hitting the phone and find a Ford dealership and speak to the service department. Just call all of them in your area and see what they say, you might even have to talk to a few different people at the same place. If this problem is not your fault from abuse, stand strong, don't let them push you around. When they question you about a chip just tell them the truth. Tell them exactly what you have done to your truck in the way of Mods. If YOU have done nothing to the engine there is no reason for your warranty to be void.
Here is the scoop on my truck.
I bought it used from out of state. I should have been smarter about it but I really wanted this truck. It was delivered to my front door from Texas to Utah. I started it up and it was putting of white smoke. I thought maybe bad gas or just the bottom of the tank, because it had been sitting for so long in a wharehouse. So I drove it down to the gas station to fill up. After fill up I headed home and the check gauge light came on. I didn't notice anything at first until the temp guage started to creep up. I only had to go about a mile and half home so I thought I could kind of coast there, then BAM!! The temp buried itself hot and I started to lose power when the "fail-safe" cooling system kicked in. I made it home and topped off the coolant, which had been way to low. I tried to drive it over the next few days only to find that with the abundant white smoke came loss of coolant, and everyone on the road hated me and my obnoxiously smokey machine. From my own suspicions and casual questions to mechanics I began to fear blown head gaskets. I read up on my warranty and there is a 5yr 100k coverage with $100 deductible on the 2004 6.0L Diesel Engines which specifically covers gaskets and seals. Now my truck had a lot of mods done before I bought it. I do not have a chip but it does have a K&N cold air intake and a 5" Magnaflow exhaust. The first three dealerships I called told me that the intake mod "could possibly" void the warranty because ford is particular about the intake system. Considering the wad I had just blown on this truck I was starting to panick, not knowing what the hell I would tell my wife. The fourth dealership said that the intake and exhaust were a none issue for the warranty but that a programer chip would VOID EVERTHING. I left my truck with the shop honoring my warranty, they asked me repeatedly if I had used a chip in it. I kept telling them I just bought it and put less that 20miles on it. After taking the truck in they told me it was head gaskets and EGR cooler and that this was a direct result from using a chip. But because there was not a chip in it now they would go ahead and do the repair. They also told me that the head gaskets had been previously replaced at 16k. I asked what could cause such a major malfunction and they said they see it from chips everytime. They said they could tell there was previously a chip from wiring and bracketry left behind, which I don't entirely believe was there. I think your truck should be under warranty and the gaskets covered. Here I am with gaskets replaced at 16k and 39k and only paying $100.
So, sorry everyone, a bit long winded, but I had to get it out.
I'll get my truck back on Wednesday and will baby her the rest of her days.