I am just going to leave this thread at people should check for that wire between the alternator and starter. That wire is a Yanmar factory wire because they assume there is only 1 battery bank. It which case the alternator cable goes to the the lug on the starter and then the power feeds to the battery. It shroud be removed during installation if the boat has more that a single battery. Mine wasn't and maybe others should check to see if it wasn't on theirs.
There was no help provided in this thread. Even when I posted the answer to the problem I got trashed. I wouldn't be posting another ever!