For starters GT40 heads have larger valves 1.84 intake and 1.54" exhaust valves. Also the port casting is much cleaner and smoother, plus the HUGE thermactor air injection bump is gone in the GT40 heads. Also they're faster burn heads because of a revised combustion chamber. I've heard that the aftermarket GT40 heads (cast iron) are supposed to add 30 horsepower to even a stock mustang GT. You can get used GT40 or GT40P heads for VERY cheap (the P heads were used on '96-'99? 5.0L explorers). GT40 heads were originally used on Cobra Mustangs and the 5.8L lightning and also sold through Ford Motorsport.
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem 
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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