Both my '49 and '53 are titled by the engine number. I called the state of Wisconsin and they told me is was proper procedure back in the day to use the engine number. They also said that as long as the original engine is still in the vehicle its easy to change the number on the title to the vin #. All I have to do is make an appointment with a state patrol officer and have him do a VIN check and sign off on the form. It can be done if the original engine is gone but they said its more difficult.
Good Luck
Don