What are the main differences between the 99 lightning and the newer trucks? Do the 99' respond just as well to mods?

What upgrades were done during the gen 2 lightnings? the earlier trucks seem to be much cheaper, even with similiar miles.

 

Here's a good site that spells out all the differences.
http://www.austinsvt.com/lightning/gen2data.html

The big highlights in the differences between the '99-'00 and '01-'04 are things like:

Bigger MAF
More aggressive ECU settings
Painted mirror caps with integrated turn signals on mirrors
Aluminum drive shaft
3.73:1 instead of 3.55:1 final drive
Clear SVT specific headlights, turn signals, and led 3rd brake light

The later years also have minor interior differences that change every year.

The power difference, 380hp for '01 up and 360hp for '99-'00, are a moot point when you mod both vehicles equally. A '99 with a 4lb pulley, intake, and chip should put down real close to the same numbers as an equally equipped '01 up model.

 

a gear swap between a modded 99-2000 and a newer model will make them about even. I have a 2000 and personally like the newer lights so i swapped mine over. Still think the 2000 wheels are the best looking.