Some times the simplest things can turn into your worst headaches, simple things, you may think. This particular event has taken place more then once and will continue to happen until it is explained and corrected.
These vessel have had continual add on's as the owner could afford it and it was old alternator which has put out for many years and it was simple right?
The former alternator was a Leece Neville 24volt 110 amp, model 8LHA3056, which was a good one so I went for another. When I was at the dealers I picked up another Leece Neville 24 volt 110 and, model 8 LHA3161. They looked the same, it was easy to install and it appeared to work.
I learned a lesson here, good ammeters on the output of an alternator are very useful tools to maintain and cycle deep cycle batteries. You see it was not apparent but the "Turn On" speed of the old alternator was 1000 rpm but the "Turn On" speed of the new alternator was 1400 rpm and it was not charging at idle.
Now with two alternator ammeters I can tell the minute one goes into failure. Additionally, I can pick the spot to drop the pick and still keep batteries up using bridging through manual control of the charge relays.