Stamping the engine and tranny with the VIN is something that hasnt been around real long. To my knowledge, I never remember seeing the VIN anywhere on my engine, unless it was a sticker that came off.
I checked into this same thing, when I was looking at swapping out my engine. I checked with someone here on StangNet who used to be a California Smog referee. The block has a part number on it, which tells you the kind of car the block was made for. But there's no VIN number that identifies that exact engine with an exact frame.