[k-luther]

I have a 2012 Yamaha F40 tiller on a 15' x 6'4" skiff with a Yamaha performance stainless 3 blade prop that is 10.5" diameter with 13 pitch. I am only getting 3600 - 3800 rpm wide open with one person and minimal load. Any suggestions on what to do for better performance? Thanks.

 

[Brett]

Check for fuel system blockage. I don't think it's the prop.
I'd be looking for a dirty fuel filter or an air leak restricting fuel flow.

 

[crl.wms]

Something is definitely wrong.  An easy check is on GPS speed.  If the RPMs are correct with your gear ratio and RPM you would be running 21-23 mph.  If you are running faster than that, then the tach may be set for 4 cylinders instead of 3 cylinders.  Alternatively, that prop should deliver 31 - 34 MPH if the boat+engine can deliver that speed at target 5500 RPM.
As Brett noted, if the engine isn't getting fuel, is sucking air or the throttle linkage is binding all could be a problem.  But it is easier these days with a handheld GPS to check speed first.