To me it seems logical that the VIN would not match the engine number, since, on an assembly line, a car could end up with a number of engine choices. Matching the numbers would require that the engine number be stamped just at the point of installation.
Since you have given your best effort to finding a VIN on the motor, I think you have no choice left but to show the engine to the cops, and let them see if they can find it.
I believe the idea that they are going to jump down your throat for having this engine is way off. Detectives usually appreciate it when a citizen offers help and cooperation. If they treated every citizen as a criminal, they would eventually make their own job more difficult. It would be different if they caught you trying to sell it, and it turned out to be hot.