When my motor was installed an aluminum plate (bearing the name of the dealer naturally!) was placed against the transom spanning the two upper bolts. This was not the case with the motor that was on the boat when I purchased it (1994 Evinrude 60hp). Although I'm asking you to speculate, is it possible that the plate is creating a more rigid surface at the level of the top bolts, leading to greater transmission of vibration from the engine to the transom? Does Evinrude recommend the inclusion of this plate?
I doubt it, your boat harmonics seem to be the main culprit. The 60 has been in production for over 13 years now and the popular 2-cylinder inline design for over 65 years in outboard motors.
"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.