The 4.6L motor has a much better reputation then the 5.4L. You should not see much difference between them using a pickup as you described.
The year range you listed (1998-2002) had many problems with the Ford 5.4 engines spitting out spark plugs and ruining cylinder heads. A very good friend has a 1999 F250 and he had the plugs come out at 67K. He replace both cylinder heads. At 97K the right cylinder head cracked and over heated the motor. He had a new long block installed and has not had any more issues. What really was unusual is that his truck is used very lightly, rarely ever pulls a trailer or hauls anything heavy. He also has had a lot of trouble with the four wheel disk brakes. He has had to replace the rear calipers twice already. They seem to stick and not adjust. I have heard that you need to use the parking brake to keep the linkage freed up on the adjusters.
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Today's Featured Article - Good As New - by Bill Goodwin. In the summer of 1995, my father, Russ Goodwin, and I acquired the 1945 Farmall B that my grandfather used as an overseer on a farm in Waynesboro, Georgia. After my grandfather’s death in 1955, J.P. Rollins, son of the landowner, used the tractor. In the winter 1985, while in his possession the engine block cracked and was unrepairable. He had told my father
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