From your description, it could be a faulty regulator. Make sure there are no wing nuts on the battery and that all grounds are clean, shiny, and secure.
If the problem continues, you may need a tech to ride along with you while they have the diagnostic software connected to the motor with a laptop and monitoring it before and as the problem develops.
"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.