Wow. Thank you for all the suggestions. Sadly I have "avoided" using our boat until I sorted this issue out as I was afraid I was going to do some permanent damage in the thousands. I am still going to follow the suggestions which all have the common theme of disconnect, I'll replace cable while doing so, and adjust settings. I'm a little hesitant to play with tranny fluid because if I get that wrong it will definitely be bad. How hard is that anyway, changing tranny fluid that is?
The engine is a yanmar 13hp 2gm. No idea of other specs.