Some good advice so far. I suspect fuel issues. The 6.0 is very sensitive to fuel pressure. Always use OEM fuel filters on the truck. also use only OEM oil filters. I would recommend cleaning the EGR valve. Unplug it, remove the 2 hold down screws and wiggle it loose. It can be stubborn but it will come out. The truth about your new elbow; no help there. The only performance gains there are at the sellers bank account. The stock intake system on the 6.0 has been independently tested against all the major intake aftermarket systems. It has been proven that until you reach 3700 rpm, no increase in air flow. The OEM Donaldson filter also filtered measurably better than any of the aftermarket stuff. A full 4 inch turbo back exhaust system is a great modification that lowers EGT's and increases turbo response. Here is a long writeup I prepared a while back on the 6.0. By the way, I have never seen a Ford 6.oh no...
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Regards