Is it bad to have a car with a lot of miles but new motor?
Is the motor the only thing that could go wrong with a car? Of course not, right? I'd especially worry about the rest of the drivetrain if you're thinking about pumping an EXTRA 140 ponies through it. If you do this, plan on replacing the tranny and the rear end . . . soon. it'll also be tough on the exhaust system, it might be worth noting here, the exhaust on that car costs a small fortune. The catalytic converter is in an "x" pipe that contains two resonators and two cats that all have to be replaced as an assembly. It's over a grand just to get that "x" pipe replaced.
Then you've still got the unrelated parts that will go bad on an old Ford. Electric windows, radio, power seats . . .
After it's all said and done it would have been cheaper to get an '03 cobra with 50,000 miles. Plus you get the independent rear suspension and massively upgraded interior that GT's so badly needed.