Sorry, you are having troubles. Using your new Honda should be a rewarding experience....not painful.
My recommendation is that you take it back to the dealer and have them check it out.
These engines are pretty darn quite. It could be something wrong with the engine or.....
It could be prop rattle (especially if it is a stainless prop).
It might be a sympathetic vibration where the engine resonates the boat at a particular rpm.
Switching to an aluminum or different brand of prop might help, if it is the prop.
I have had on a couple a situations, a prop that rings like a tuning fork while moving at idle speed. It almost sounded like something internal to the motor. Fortunately, I have a musical background and on a hunch, remembered the tone as I pulled it out of the water. I immediately went back to the prop and flicked it with my finger. It had the exact same pitch, etc. Changing to a different brand of prop fixed the problem.
It might be just the shift cables vibrating against the boat.
In general, the Hondas are so quite compared to the two strokes, that you can hear noises on the boat the you could not hear before.
I know I am rambling....but definitely contact your dealer. Did they not water test the boat and hear it themselves? They should have to be sure it has the correct prop.
Did they go over the PDI (Product Delivery Inspection) sheet with you? It is a check list of all the things looked at when you installed the motor and a check list of what you go over with you when you pick up the motor. Both you and the dealer should have signed it and you should have received a copy.
It will state full throttle rpms, prop type and size, etc.
There should also be a computer printout from Dr H or HDS, that you get showing all the parameters of the engine as it is running.
If the problem does not get resolved to your satisfaction and you are in the USA, contact Honda Customer Relations to get help from that angle. 770-497-6700
Good luck. Let us know how things go.
As always, hopefully, others will jump in with their thoughts.
Mike