Lets say someone along the life of the car lost their title. They went to the county they live in, and got a duplicate. Usually just about $5, and 10 minutes at the courthouse. Then the car gets sold after the old guy dies. In his collectables which get sold later, to a differnt person...that title happens to be stuck in something else...tool box, a manual, etc. That person sells the title on e-bay. That person made that title over for their car. Then you come along later, and because he was first you appear to be out.
See if you can find out what the process is in your state to get a title to a car if you want them to assign a VIN. Just tell them you have a car that the engine was changed in. Sometimes they will send a highway partol officer out to look at the serial number, and you will have to take the coach up, and block it out of the way so you can wire brush the area, and he can see it. In my county if you need a VIN assigned you have to file a court case ($250) and meet with the judge before the officer will even come out. Now days I hear they make you tow the car to them. If you still have your bill of sale, canceld check, whatever, that helps a lot.