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What says you? Used 1998 4wd 4.6 high mileage on the cheap or a newer f150 low mileage with the 4.2 ? 2500 for the high mileage or 7000 for the newer? 98 has straight body and is unmolested as is the 2006. Plan to use as a truck/backup vehicle, pull a boat, home depot run / weekender. My thinking is 98 with the cost I can always swap in a new motor and trans and still be right around the cost of the 06 but have a new drivetrain. Question is, do reman motors have heads that fix the spark plug spit issue? Any expensive issues I am overlooking with the 98 model year? Heater core? What else?
How big is this boat?? Hope that your boat is not very big or you intend to go very far with it in tow?? V6's are not know for their towing capabilities, but would make a great weekend utility truck to do those odds and ends tasks and a back vehicle. The 06' is a bit wider and longer then the 98'. So interior cab room of the 06' should feel a bit more spacious. The aftermarket support/ parts will be greater for the 06'. With the 98' the aftermarket support is there but starting to dwindle a bit because of the age.
As far as the spiting spark plugs out on the older ones....that issues was largely due to too low of torque rating early on from the factory on the spark plugs....now suggested for 28ft/lbs. The later 03' redesigned heads did offer more threads in heads which was helpful as well. Plus after 2000-2001( or some where in there), Ford made Power Improved head ( aka PI head). SO IF...you decide to get the 98' and drop in a reman engine...be sure to get the latest heads available for that generation.
In a nut shell, either one has their strong points and weak points. It really is going to be what fits your needs and what you going to be comfortable with. DO some more research and post up what you decide....good luck!