The prices of the sensors included phones does make "instrumentation" spec gear look insane. Difficult to get away with paying less than £500 for each microphone and triaxial accelerometer for industry and then the cost of sending back them to the factory every year for calibration and certification.
The phone's 125Hz divided by 2 for a four cylinder four stroke engine firing twice per rev comes out at 62.5 revs per second or 3750rpm. Right on Dan's boom problem rpm range.
Honda's use of a solitary quarter wave tuner "nob" is a bit unusual in my experience. Maybe there wasn't room to package anything else in that spot. Most Helmholtz and similar tunning features are hidden away in the guts of the silencer.
I'd have thought a little "hotdog" expansion chamber in the same spot as the nob would effectively break up that 125Hz standing wave in the exhaust.
The replicated "quarter-wave" nob may not have worked as they have a narrow effective frequency range whereas a broad necked Helmholtz will help a much wider band.
Kudos on the maths Dan and the deepest envy of your fabrication skills.