Glad you got it running.... but you are backwards on the filter names
The one in the HFCM on the Frame Rail is the Primary Fuel Filter / Water Seperator, and the filter is a 10 micron filter
The one on the engine, next to the Oil Filter, is the Secondary Fuel Filter, and the filter is a 4 micron filter.
Also, did you remove the drain plug from the lower front right side (Next to the Transfer Case) and drain all the water also?
How many miles were on this set of filters, you should change the fuel filters every 10,000 miles. That will help with any fuel related issues.... the 6.0 does not like dirty fuel at all......