Can I get my motorcycle back?

I bought two motorcycles as parts bikes from a guy out of state. One bike had a title and the other one didn't. So I took the good parts off of the bike without a title and put them on the frame of the bike that had a title. After months of working on the bike I finally got it running. I ran into a little snafu with the title though. The two previous people on the title never registered it. So after a little digging I tracked down the last owner who registered it and he went and got a new title for it and sent it to me. I did some more work on the bike and finally got it road worthy. So today I went down to get it licensed and when they run the VIN it comes back as stolen from 2009. So after months of work my motorcycle is sitting in a police impound lot. Is there any way to get the bike back? Also, why didn't the bike come back as stolen when the guy applied for the new title?