I'm currently an engineering intern in the Sustaining Engineering group for Remy incorporated, an alternator remanufacturer. One of the alternators we deal with on a regular basis is the one your car came with.
I'll make this short. The older S198s use a 6G alternator. They have quite a few problems, and Ford didn't do a great job designing them. I can think of at least three major warranty issues off the top of my head.
Alternatively, the newer S197s came with Denso alternators. Denso is the competition for my company, so I don't say this lightly, but they make a better product. It's more expensive, but higher quality because much of it is manufactured in the US, not Mexico or China.
As a third option, you can pull a Mitsubishi alternator off a police interceptor with the same 4.6L 3V modular engine. That alternator was specifically made for those cars, and is rated at 215amps instead of the 135amps from the stock alternator. As a plus, you could probably get one at most auto parts stores.
