Yeah, there is a shortage of mod V8s for the Mustangs. The demand for V8 Mustangs is much higher then Ford thought, plus a lot of the V8s end up going into trucks and SUVs. There's much more profit for trucks, so that's where the engines go.
Don't pay a premium to a dealer. That's just them wanting more money. Look around some more, and you'll find one for a resonable price.
http://www.edmunds.com/newcars/2000/...g/gtcoupe.html