Mine never had the recall done either.
Here is a link to probably the best place to get info on the 99 recall...
http://mysite.verizon.net/txsnakecharmer/techman1.htm
As stated by Cobra90GT, call SVT to have the VIN checked. While you are on the phone with them, order the certificate of authenticity for your car if you didn't get it from the last owner. Mine never had the recall performed, but SVT says that not all 99's suffered from the lack of power. I took mine to Kauffman Motorsports and had it checked on the dyno. With a JLT cold air kit and
Flowmaster cat-backs, I put down 277 rwhp. That’s around the target range for a stock 99, so a good intake and tune should have netted around 300 rwhp.
Most guys around here (PA), say the intake system will hamper you about 10-15 horsepower by itself. I bought a cherry extrude honed/hand polished intake manifold setup (TB, upper, and lower) from Justin at JPC. He used this on his personnel Cobra until he went pushrod. Unfortunately, my connecting rod shattered 2 weeks before I was having the intake swapped, so I bought a new Mach 1 crate motor from Ford. If you find yourself wanting to replace your intake manifold, give me a shout.
ALSO, DO NOT TOSS YOUR OLD INTAKE!!!! 03/04 Cobra owners need these intakes when doing turbo swaps, and they are in short supply. Someone will buy it as is for their project and have it ported. Best of luck!
George