If its a daily driver, i would go ahead with the GT. The 96-98 4 valve cobras are nice but not as powerful as the 03/04 so it wouldn't really be worth it, and you'd be saving alot in fuel with the GT as well.
Cobras did not begin until 1993 making them the first Cobras from SVT but the last fox body's. the 96-98 Cobras were of the dohc 4.6 motor which the cams were inside the head making them NOT Gt40 heads. Those died with the push rod 5.0s.
Like i said, you're better off going with a GT because its newer, might find one with lesser mileage and would be better on gas. Its all up to you. But that's just my recommendations.