01 and up GTs had the different side scoops and a scoop on the hood, where the 99-00 just had kind of an indention in the hood and scoops. There are also some colors available only specific years. Taillights, I'm pretty sure, were all the same. It seems like in 01, there was a slightly smoked headlight. I could be mistaken. I kind of lost track of options after that year, as I bought a car and wasn't still shopping around. There are some slight interior differences. Someone I know had a 99 V6 convertible, and it was a little different layout than mine. Nothing major, though. There are different spoilers through the years as well.

I'm drawing a blank, but I don't think there's much/any difference performance wise, if you're strictly talking 99-04. I see you say 2000, but I don't know if you mean that year or if you are unaware that the first year of that body was 99.

The side scoops are interchangeable. The previous owner of my 01 put Bullitt side scoops on it. I wanted to put the stock ones back on, but never did. People apparently steal side scoops off people's cars, too.

Browse eBay and look at pictures of varying years. I prefer the 01 and up look.