this has been discussed in depth over at the Hi-Po Mustang forum.
http://www.hipomustang.com/
In my view, stamping VIN or serial numbers on the engine may not be fraud, but it is, or will be on down the line, a mis-representation. That makes it not ethical. Even if the replacement block has the correct date code, it still is not the original engine to the car. And, rightly or wrongly, a car having the original engine will be worth more.
So the temptation exists to pass off the car as having the original engine when in fact it has a replacement engine.
My view may be in the minority.
Z. Ray
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'66 GT-350
Original Drivetrain, Sheet-Metal, Interior, & Paint