There are a number of places where a short could occur both in the boat or on the engine.
Your motor is within the 3 year warranty period, I assume, so if nothing is obviously shorted that you can see, allow your dealer to troubleshoot and repair what is needed.
EMM (engine computer) failure is pretty rare but have your dealer check a few things that could have contributed to the problem.
If the engine report indicated that there were EMM over-temps, have the EMM and vapor tank cooling lines and fittings cleaned out. If they also happened during engine overheats, then the whole cooling system and water pump assembly should be inspected and/or replaced.
Make sure that there are lockwashers and hex nuts fastening the battery cables - no wing nuts !
Check battery for proper capacity and load test.