differences between 96-98 and 99-02 cobra

You'll want to check out SVT's homepage, go to the "cobra" section, and then click on "view specs" for each model year cobra. Lots of information.

96,97,98 (Naturally aspirated).
99,01 (Naturally aspirated).
03,04 (supercharged).

The best mod to help these cars are gears. 4.10s or higher. 4.30s or 4.56 if you are serious at the track - torque multiplication.

you would only have trouble with a GT if you're a poor driver.
yeah you'd stay about even till the end of 2nd gear, then once the cobra hits 3rd it's gone. my friend and I raced both stock 03 GT vs. my 98 cobra. i'd kill him after 3rd and from a roll he didnt have a chance. now my current mods vs. 03 GT with bassani catted x and bassani catback i destroy him all the time.

solid rear on the 96-98 compared to IRS on the 99/01.
better interior in the 01. 99 is lame, like 96-98 but still comfortable.
just really different intake manifolds on the 99/01's to get that extra power and pull a little harder up top. they're pretty even cars though. depends what you like more. i went with the 98 over 99 but i'd go 01 over a 98. and 03/04 is def. the best all around.
on the other hand, the mach 1 is the best choice if u want an N/A cobra.
solid rear, cobra motor, sick interior, ram air. goin to look at one tomorrow actually.

C heads on the 99-01 b heads on the 96-98. I like the 98's cause they are lighter than the 99-01's and the b heads are good for boost

I ran my stock '97 Vs. an 04 GT modded with cat-back, CAI + MAF, pulley's and ECU tune. He had me by a couple of cars until 3rd gear when I started creeping back up on him. We both maxed out at the top of 4th gear and I just held it steady with him. Of course the second I edged past him (intentionally) he backed off.

:NOTE: This was a deserted highway at 1 AM in Arizona. Don't try it in areas with any traffic.