Honda has been making their own lower units since the late 90's. They only used the Mercury gear case the first 2 or 3 years of the life of the 75/90.
That motor tends to have a rattle type sound especially if you are trying to run it out of the water (on a hose) and especially if you have a stainless prop.
Generally, this rattle subsides once in the water and the prop loads the gears. Of course, you should check to be sure that the prop is on tight.
Since this appears to be a repower, replacing a two stroke motor, there may be sympathetic resonance causing some part of your boat to vibrate, especially at speeds at an idle or just above an idle. In other words, there is a vibration in the motor at a certain frequency and it not only causes something on your boat to vibrate at that same frequency, but also amplifying the sound. It is like in school when you had two tuning forks and the vibration (sound) from one caused the other one to vibrate and make a sound.
Since the Honda is so quiet, these sounds show up pretty often, especially after a change from the noisy/smoky two stroke that was taken off.
If the chatter continues, sometimes changing the gear lube to a high performance gearlube (like Mercury High Performance Gear Lube) will help smooth things out.
If the sound is more like a ringing type sound, changing the prop might fix that. I have had some where an aluminum prop rang and caused the engine to ring and it sounded like it had a problem. Flicking my finger on the prop ear emited the same note (as in musical note) as the engine was sounding. I think my boss thought I was nuts. Changing the prop to a stainless or composite prop eliminated the ringing.
So much for my "war stories".
Mike