Mine has 108k on it, and I beat on it daily. But I beat it in a carefull way. Not hitting the rev limiter ( if there even is one have'nt come close to hitting it), powershifting in 99-01 GT's is bad, tranny's suppposedly arent as good as 02-04, however i've driven both, dont see a difference. Put a good shifter on it and your ok. Anyways, I have alot of miles, and, the only thing bad about my car that I can say is, I hear a little bit of lifter noise or something, after it's been sitting(cold start). Not nearly as bad when it's warm out, go's away after about 2 minutes, and I use a K&N filter with royal purple, so it's def a problem but not one that i'm concerned about.
My opinion 4.6 2V is as good as any V8, except the 4V lol. They're good, and, I cant even imagine how long either of them would last if they were never ever beaten, just driven like an old lady. I'd say 300k no problem. As they've said above, I think...the GT's dont have forged internals, but, they're not exactly weak as hell either, just not as good at holding up to power adders. A stock GT is fine, and should last a very long time with proper maintenence. This from much experience. As far as 5.0's, I had 5 total, only 1 actually broke, in the bottom end, it had 179k on it, it was winter, a friend asked me to take him for a ride, he'd never been in a stang, or any fast car actually, so, I said sure. I made the mistake of not letting it warm up very much, maybe 3-4 minutes, went half way down the block and stomped on it in first gear, and snap, the crank in two pieces. When we took the pan off after lifting the front end way up, at teh shop, the damage was unreal, and only about a quart of oil was in it. It broke because I was a lazy ass who didnt check my oil, or let it warm up. IMO 5.0's are better, but 4.6 has better technology, ohc, I much prefer ohc to ohv. I type too much....
99-01 Cobra IMHO is defonantly better than any 99+ GT, however, the 03-04 Cobra's are absolutly sick. I've driven two, and......I cannot stress how much fun they are, sooo fast, and stock! I'd say, if you're not the type to mod a car, the newer cobra is best, it's fast enough stock to beat most any car, except another one modded LOL. If you "want" to do lotsa addy's, i'd go with the older cobra, and lastly a 99+ GT.