This is an old topic, but when searching for the fix to my 2000 GT it came up. My issue was the IAC (Idle Air Control Valve). I replaced this for $60 cheap or Motorcraft for $115 and everything has been fine. The problem is, (Car doesn't run well in the AM when its cold, or will not idle when taken out of gear. It does run fine when you get on the gas, but will not idle.) Hope this helps.
To the guy with the bogging down when you gas it, sounds like a lot of things, cracked valve, fouled injector (s), or it's getting too much air from a crack somewhere.
As for my 99 Mustang GT 35th, it's a fine running car, has 70k miles.
You have bought a high performance machine that requires attention and love, as my grandpa said "you gotta pay to play", so if you're having problems fix it. We ain't talking about a family wagon, if you know nothing about cars then this is your chance to learn. This is what American muscle cars are all about, learning and improving. Don't be afraid of your car, add some HP and love getting dirty under the hood, or get a Geo and let some cop change your tire for you.
I also have a 1999 35th Anniv Mustang GT (Black with gray leather interior). It currently has 184,000 miles on the clock and still runs strong.
Over the years it's only had minor repairs such as alternators, clutch, rear end seal and that IAC which causes the idle problem however, this is by far the best and most reliable car I've ever owned.
I also believe that these cars are faster than the 2000-2004 GT models. My fiance owns a 5 spd 2003 GT with 70,000 miles on it. The other day we raced them against each other (stang vs stang) and I was amazed with the distance the ole' 99 put between the 2003. The 99 smoked the 03.
I would advise anyone searching for 1999-2004 GT to go with the 99. Awesome car. I wouldn't mind being buried in one.