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Hi. A few more details will help. First thoughts are
are your throttle linkages adjusted correctly?
are the linkages and throttle cams in good condition?
do you have 2 engines and struggling to keep the rpm balanced?
What is your max cruising rpm on both motors at full throttle?
Do your engines idle smoothly?
Are your motors 2014 models?
im a little short of ideas for you at the minute but all this info should help when some of the other folk on here come online.
Another thought, are your tachos reading smoothly? Do they bounce around and drop off sometimes around a certain rev? Can you actually hear the motors rpm fluctuate around or are you using the tacho as your guide? I'm wondering if it's actually the motors or the tach that is really the issue. Are your tachos honda or another brand? The 3 cylinder motors have caused some tach confusion in the past.
It sounds like you should take it back to the selling dealer. Can you tell if maybe just one of the motors is running erratically? Have you checked to see how each one throttles up when it is running by itself? That might help you narrow down where the troubleshooting should start.
I also think like skronkman, that the linkages may not have been synchronized on each motor. Not motor to motor, but just on the each of the motors themselves.
I would also see if the dealer vacuum balanced the carburetors before delivery. They are supposed to come balanced from the factory, but many times they are not. The dealer should at least check each multicarbureted motor before delivery to the customer. As an FYI, if the dealer is not up to speed on how to balance the carbs, they do have to clamp off three hoses that go between the carburetors, otherwise, it will look like the carbs are balanced when they are not.
Other than an odd spot here and there, those motors should have smooth acceleration.
Check your oil level and make sure that it is not too high...ideally about 1/4" below the full mark.
Pump a sample of your fuel into a glass jar and see if there is any water in it.
Check your spark plugs to see if they are NGK or Denso. If they are Denso, replace them with NGK's DR7EA. Densos tend to fail much earlier than they should.
It is also possible (although not very probable) that one of your thermostats is stuck open. These motors do not like to idle when they are not warmed up. The 30s' thermostat starts opening around 162 deg F and is fully open at 180 deg F. If the thermostat is stuck open, it will run too cool. If you have a handheld temperature gun, measure it at the thermostat. It is just to the left of the top spark plug.
Fuel, temperature and carburetor balance are three of the key elements at the rpms you are trying to run.
Mike
Can you pop the cowling off and watch the linkages moving while you are shifting in and out of gear and throttling up/down? You may need a mate to lend a hand at the helm while you are watching the engine. No need to start the motors as you are just looking for smooth operation and no sticking or catching.
Is your throttle control box is the original honda unit for your motors?