Upon testing the alternator I discovered the diodes were blown in it. Luckily I had a back up alternator on boat.
|Shiny new alternator|
|Fitting new ground cables|
A bit more digging around led to the discovery that current on the house batteries were reversing themselves through the combiner. A Class T 300 Amp fuse near the positive side of the house batteries had blown. Replacing that led to the problems all begin resolved.