In addition to above:
Problem can not be replicated when the motor is in neutral (not under load). Engine can run 6200 RPM (possibly slightly higher) for 90 seconds without error.
I have a 2013 Yamaha F40LA that will run all day at 2200 RPM which is what we do 95% of the time on our lake. Seems to run out uninterrupted 3800 for long stretches of time as well. When I advance the throttle full forward I get between 5000 and 5300 max RPM. At max it runs out constantly...