Because I've had a 99 for 4.5 years I'm prejudiced. I made a few mods to mine and it dyno'd at 297.5 RWHP and 295 RWTQ -- and that was simply a Dynomax X-pipe and cat backs. Since then, I've added an 80 mm C&L MAF w/ K&N filter and BBK 75mm twin throttlebody. So I'm guessing I'm making more than 297.5 RWHP now, but I haven't dyno'd it since the add ons. It also has a new 3.73:1 rear end.
IMHO it's largely a matter of luck. I've heard of complaints from both 99 and 01 owners. Mine has held up great. I set it up for driving on road courses with a full Kenny Brown suspension system. I've been running it at instructional open track events, primarily at Summit Point WV, but also at VIR with SVTOA, NASA and Car Guys for the last three years. Changing the rear end allowed me to run both courses in 3rd and 4th gears vice 2nd and 3rd with the stock 3.27:1. Summit Point's main track has a 3,000 ft front straight and I've reached 135 mph before I had to get on the binders for the first turn. If you get a good engine, it should pull all the way to redline.
I've not had a bit of trouble with the 99 and power doesn't seem to be a problem. Most S4s I can run from, and the KB suspension mods combined with the horse power keep me in the pack with most M3s and C5 Corvettes. I think there's not much difference. Just get one with a good engine. And, you probably know better than I how to do that.
I beat the 99 with gears exhaust and the fix. He made 264 rwhp. I ran 13.7 @104 with those mods in my 98 on nitto's. This guy can drive.
Saw a 01 Cobra within 2 months after that with exhaust and 3.73 or 3.90's run 13.4x @ 105.xx. Supposedly he is making 285+. I am not sold on that number though, but possible.
I believe there is validity in the fact that the fixed 99 still didn't make the power of an 01.
Beat it more....show me proof in numbers and I will be sold.
I ran 13.6 in the 1/4 mi the year I bought my car with just the air silencer removed. Stock tires and all.
Many people dyno'd the 99 after the fix. I bought mine used and it had the fix.
Think about it... there was a big uprising because of a lack of power. Dynos showed the cars were down on power. Ford does a fix, you think all the owners just trusted Ford gave them the power they deserved?