I have a 97 GT. I put my blower on at 107K. I have 185K on it now and it runs like new. So it seems to me that the mod motors are pretty robust. The choice comes down to what you want to do. The 5.0 is easiest and cheapest to work on-and the power potential is awesome. The mod motors are really smooth. Nice power gain on a 96-98 by putting a blower on-pretty easy too. I prefer the 94-98 body. 99+ has the most powerful motor from the factory but will cost more. Of course a blower on a 99+ or 5.0 will make even nicer power gains! You might want to go to a used car place and test an example of each. See which one leaves a grin on your face the longest.
I helped out a friend of mine (from out of state) purchase a 94 GT. I test drove this car in here in MD for him. It was an auto with 90 something K on it. It ran like a new car and had surprising power. All this for like 6900 bucks. I have to say, I was like, hmmmm I wouldnt mind having this one also: Same looks as my car, 5.0 that could be modded swapped etc. etc. So check em all out and see what feels best.
97 Laser Red GT-248A Wingless model, Built Lincoln Mark VIII motor-Procharger D1SC, 3 core IC
2012 Black GT-Saddle, 3.73s, Brembos, Shaker1000