The problem may be simple. Since you only drive it a few miles a week the engine never gets to full operating tempature long enough to keep the spark plugs and the cylinders clean. You should drive the truck at least 10 to 15 miles a week at one time to keep the carbon from building up in the cylinders.
The 1st thing I would try is just replace all 8 spark plugs and take it for a drive and see how she runs. If this corrects the problem then I would get in the habit of either taking a 10 to 15 mile drive at leat once a week or change the spark plugs every other month.
I would definetly start with a simple tune up, from the sounds of it with 64k on it it may not have had one at all yet.
When engines get too cold it's hard for complete combustion to happen which could be what's causing part of your rough running that smooths out after it's warm. Let the truck idle for a few minutes before you drive it, but I would look into plugs and wires as well. It's generally fairly inexpensive for the repair.
Your air filter generally should be changed ever 15-40k depending on what type of roads you travel and the amount of dirt / scum it has to filter out. The fuel filter is really a preventive maintnace item. What youv'e described doesn't sound to be fuel related. I reccomend to my customers to replace fuel filters about every two or three years for newer vehicles, and a year or two for slightly older vehicles ( they generally have a larger buildup of rust and sediment in the tanks that get's trapped in the filter over time.)
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