Probably a shot in the dark, but I was reading a boat restoration thread where someone said that if the boat has never been registered/titled before in FL, you can fill out an affidavit that it's not stolen and get your paperwork started that way. Said they run the hull ID # and if nothing comes back, you can go this route. They also said you have to talk to a clerk who knows about this.
I do feel your pain. I have a couple stories about registering vessels here in TX with paperwork anomalies. Dealing with remarkably rude and unsympathetic clerks is like getting a root canal.
I've read something similar but haven't been able to get any solid information online or from clerks at the tax office. It's a pain waiting for an extended amount of time and hoping the next clerk will have more information. I've been to the tax office 3 times now and haven't made any progress. Our boat cop at the work has no idea either. I have no idea of what to do. Thanks for the help though.