I just had my 2005 upgraded after a blown head gasket and it cost $7800. There are several inherent design problems with the 6.0 that started showing up at around 96000 miles on my truck. Navistar, the manufacturer of the 6.0, and Ford had a big court case over the problems after Ford paid out more money per unit in warrantees than it had on any other engine it ever built. Navistar said in the court case that they had designed the engine as a 300 hp engine and Ford had cranked up the fuel and turbo to 340 hp to be competitive with Dodge and Chevy. Ford responded that the engine was just poorly engineered and prone to trouble.
Ford didn't reveal a lot of the issues to the buyers and, in my opinion, intentionally covered up some of the issues to prevent pay outs of warrantees. As a result, my blow head gasket was 'misdiagnosed" by the dealer until the warrantee on the engine expired. At that point they were more than willing to charge me $8000 for repairs.