I doubt I can help with specific advice on the electronic Cummins, but there's a trick I use in my shop to find shorts:
Get your multimeter and set it on "beep". Connect the black lead to ground with an alligator clip. Clip the red lead to the "load" side of the fuse. The meter will then "beep" continuously due to the short circuit.
Now go through the wiring and wiring harness, wiggling and moving all the components and wiring bundles. The instant the "beep" stops, you've found the place that the short is located.
Like the others, my hunch is you have a chafed wire someplace, probably in the instrument panel (do you have a panel on the flying bridge?) or the harness to the engine. The chances of a short in the harness that is integral to the engine is pretty low.
John R. Stewart
"Rise 'n Shine" Prairie-29, (formerly) "Driftless" Albin-25, Hull number 737
Dighton, Massachusetts, USA