I just went through it in Michigan, I bought a 2003 400ex wrecked just to fix it up and make some money, the original owner who I bought it from had lost the title, he wrote me a bill of sale but they said it wasn't enough, they wanted him (the original owner) to come in and apply for another title and then sign it over to me, the original owner wasn't willing to go through the effort (because I hardly paid him anything for the quad) and I ended up applying for a new title myself. I don't exactly remember the forms I had to fill out but the police had to come out to the house and verify the VIN #, it was a big mess.
It might be different in your case since you bought it in a state where they don't title quads, there is no original title so maybe the bill of sale will do.