I bought the boat and have a Bill of sale, but there seems to be some
confusion about who actually has the transferable registration. This
boat has changed hands about three times without the paperwork following
it, once through a boat dealer.

At this point, you have a disputed ownership interest in the boat- at best.

"About" three times? Are there people in the chain you don't know about?

Fortunately, the fix isn't all that difficult.
You won't need all the intermediate parties to sign off on the title or
registration because they never legally owned anything. As far as the state is
concerned, the guy who sold you the boat didn't own it. You will need to track
down the last party who had the title and get them to sign off. Just hope you
don't discover that the boat was stolen out of the last registered owner's
driveway.......

You can also thank your lucky stars that there was a dealer involved with one
of the transactions. Is he/she still in business?
They may be sitting on the title, having overlooked doing the transfer. If CA
is like WA, the dealer's chestnuts could be roasting on an open fire if he/she
sold the boat without valid title. I would think the dealer would have a
sincere interest in helping you solve this problem with as little attention
from the state as possible. :-)