I had the same problem of backflow into the bowl, replaced the hoses and joker valve but still had backflow into the bowl. I added a valve to the line and shut it off whenever I leave the boat. Interestingly it fills the bowl but never overflows the bowl when the boat's not rocking...I guess there's just enough in the hose to fill the bowl. Seems like the leak has finally quit and I'm not sure I need the valve any more, but I'm still going to close it off when I'm gone.
A marine head service guy told me that vinegar and oil was good for preventative maintenance, but not for clearing out clogged lines. He said some people use muriatic acid. Has anyone done that? Any luck?