This could be caused by the fuel filter. If the fuel pressue is low due to a clogged filter, it will cause an "altered" idle.
I would change the fuel filters with a set of Motorcraft filters. That is all that I will use. I also use power service (Silver in summer, white in winter). I have also heard good reviews on Howes.
Maintenance on a 6.0 is CRUTIAL. I would go no longer the 5000 miles on the oil, if you are using a dino oil. No longer than 10000 on fuel filters. Only Motorcraft filters, and a high quality oil, I actually use the Motorcraft oil in the 5qt jugs. Also run only quality #2, or B20 or less. DO NOT RUN TRASH FUELS IN A 6.0L!!!! You WILL DESTROY the injectors. Buy your fuel at a station that has a high turnover (busy, sells a lot of diesel). Trying to skimp on a 6.0L on maintenance or fuels, it WILL cost you.!!!!
Also, as mentioned above. Check for boost leaks. If you have a split or blown boot, or have a crack in the charge-air cooler (intercooler) it will affect power and cause the truck to smoke. You may have to pressureize the system to find leaks, as it may only leak at higher boost pressures. Make sure all the metal boost tubes are seated in the boots and have not blown out of a boot.