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Hey there, I also have a 99 F350 Powerstroke with a 6 speed. It too runs bad at low rpm's but after about 1,500 it takes off. I have been looking into it for a while and the biggest thing I have found is that the #8 injector has a tendency to go out, or spudder. When I bought the truck at 188,000 miles it ran fine. About 195,000 miles the problem showed up. It now has 232,000 miles on it and it has not gotten any worse, but then again it has not cleared up. I hate to say it but your injectors might be going out like mine are. I have checked everything on the truck and talked to several different people from Ford Dealerships, local mechanics, to high preformance diesel shops and they all come back to the same responce. I am getting no odd reading from any of my gauges that would lead me to think that something else may be causing the problem. Well I hoped that helped, and good luck.
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