if you have a bill of sale, you're entitled to any information they have on the legal owner. i've titled many bikes with lost titles here in oregon (including my rider), and though it's a pain in the ass it's doable. i'd go in without the bike and show them the bill of sale. if there's a lien or something else wrong with the situation, they'll tell you.
if your bill of sale is for the other VIN number, you can just get a proper one for your frame and go from there. a "proper one" is any bill of sale saying that someone sold you the bike (i'll "sell" it to you if you want). the reason they're wanting to see the VIN is because you have nothing saying the actual bike is really yours.