99-mid 01 GT's still have the crappy non-aluminum crossover intake manifold that is almost garunteed to crack and need replacing.
Mid model year 01+ got the aluminum crossover.
99-mid 01 GT's still got the T45 transmission from the 96+ model year. Its not as "strong" as the TR-3650 that the mid 01+ GT's got, but my God does it have many less issues. There is a zillion page long thread on people having problems with their 3650 transmissions. Hardly a peep about a troublesome T45.
99-00 GT's (possibly through mid 01, but I think late 00 was the cutoff) had Windsor 4.6's, 01+ had Romeo engines. The Windsors are supposidly a little more stout in the bottom end, but ive seen a decent amount of posts about people spinning bearings in 99/00 GT's as compared to 01+.
Thats all I can think of really, im sure soeone else will have something to say.
I know you said 02+, but the 01's are the same as the 02's basically, and I figured id give the heads up about all 99+ 4.6's.