My friend's motor was doing that. We went through the fuel system and couldn't figure it out. Finally we were able to determine that the motor was over revving and the engines protection system was shutting it down. We changed the prop and never had any further issues.
Capt. Craig Copeland
2013 Nautic Star 2110 Shallow Bay Boat
Nautic Star Boats Pro Staff (nauticstarboats.com)
Redneck Fish'n Jigs Pro Staff (redneckfishn.com)