Tuesday - last edited Tuesday
A gentle surging is most often a fuel delivery problem and a sharp on and off surging is often an ignition problem.
It has to be determined first to if it is fuel or electrical and troubleshoot from there.
Was the motor installed, setup, and tested by an authorized dealer or did you do the work yourself?
Was a fuel system vacuum check and air bubble monitoring performed while observing fuel pressure readings from the pumps on the engine?
That fact that the CHECK ENGINE light came on says that it could be water in the fuel or some type of electrical problem. The engine would have to be run using the diagnostic software for reference.
If you are doing this yourself, please obtain the factory service manual and follow the factory approved troubleshooting tools and procedures.
"There is never just one thing wrong with a boat";
-- Travis McGee, main character in a book series by John D. McDonald
The factory recommends that a properly trained technician service your Johnson or Evinrude outboard motor. Should you elect to perform repairs yourself, use caution, common sense, and observe safety procedures in the vicinity of flammable liquids, around moving parts, near high-temperature components, and working with electrical or ignition systems.
The information offered here is only general in nature and should not be construed as complete factory approved procedures, techniques, or specifications. Always use the proper service manual for your motor, up-to-date service literature, the correct tools, and have an understanding of how to proceed with troubleshooting and repair methods. If you are unsure or uncomfortable with a procedure, a situation, or a technique, enlist the services of a factory trained technician.