Brad,
Yes, fuel filter changed and seems truck is running smoother, I also had experienced a couple of hick-ups in rpm occasionaly while cleaning. Next I want to tackle the sediment filter, and rinse it out per the one guys directions.
Oh by the way Jim thanks for the advise on filling the filter with diesel I wouldn't have done that other wise, so you saved my arse.
This water issue was (believe it or not) a drain line from an ice machine that had come out of the drain and there was this much water just overnight.