It's a common problem with old cars and trucks as many states used the engine number as the VIN well into the 50's, if not later. The 50 3/4-ton I bought in 99 from a MO guy had the original engine serial on the title but already had been swapped for a V8 when he bought it 12 years earlier. He had a good MO title, it just didn't match any number found on the truck. MO had a special form the seller could use to explain any discrepancies. With that I had no problem getting a KY title.
Try to explain that the number on the title is apparently the original engine number and that the engine has been replaced...
Good luck.

Professional Novice