[fiveohpatrol]

The 01, even being an auto, will murder the 98 in performance. The 96-98 heads/intake are way under par to say the least. In 99, the 4.6 got the PI (performance improved) heads and intake. They greatly improved the performance of the previously weak SOHC 4.6L
Slapping a set of PI heads/intake on the 98 would not be TOO difficult, nor would it be too expensive.
So its really up to you in what you want to do.

Are the two cars the same price? Do you prefer one of the body styles over the other?

If it were me, and depending on their price, I would either get the 01 and swap a 5spd into it, or get the 98 and put the PI heads/intake on it.