People don't sell a 42 foot twin diesel powered crusiers because it has a "short".
Ryan, the fluctuating voltage could be driving the engine control computers nuts. Given the ECU's, and the electronic throttle and gear controls, you'd be smiles ahead by having a qualified Cummings mechanic have a look at it. He'll plug his diagnostics computer into it and likely find the issue - or at least narrow it down to some possibilities. Could be nothing more than that the control units for the engine(s) or throttle need a S/W update.
There is another boating forum that specializes in diesel related issues;
http://boatdiesel.com/. Might wanna run your issue past them.
Dan