Yamaha F115 limited power, surging, and vibrating

[Trailerlife]

2013 4 stroke Yamaha F115 acting up. 84 hours on the motor, only use ethanol free gas.
Symptoms: started surging intermittently at irregular intervals, dropping 500ish RPM and slowing, then surging back to previous speed. That grew into not being able to get above above 1000 rpm, bogged down and not getting on plane regardless of how far throttle is advanced. Idle is slightly rough with vibration and some surging. Here’s the weird one, with the transmission disengaged, there is full throttle control and rpm goes up just fine with an only little extra vibration. No problem starting and never cuts out.
Annual maintenance 10 hrs before the issues: new water separator, new inline fuel filter, oil and filter change, new lower unit seals and gear oil, new impeller.
Troubleshooting since the issues: new VST filters, cleaned and tested injectors, stamped and inspected prop and bearing to check for spun prop.
Open to all insights and insults.

[99yam40]

motor needs more fuel to run under a load, so it sounds like the cylinders are not getting the fuel they need under load.
check rail pressure to make sure it stays in spec as you raise RPM under load.

And make sure your warning alarm functions properly.
if there is a problem but you alarm does not work you may not know the motor is in PRM limiting mode.

do you have gauges to indicate there is a problem when there is one?

[Trailerlife]

I don’t have gauges or know what to check. Would it make sense to replace the fuel pump? I know not the best way to troubleshoot but given my experience level and resources it seemed like the next step.
Thanks for the point about the alarm. How do I check that? If it was in rpm limited mode would that still be in effect with the transmission out of gear because I’m able to hit 4K + in that mode.

[99yam40]

I believe if you pull the man overboard kill switch clip out and then try to start the motor the alarm will sound to test it.
and I agree with that should limit PRM any time, but not positive that is true..
do a search on measuring rail pressure,
if the fuel pump was a problem, pumping the primer bulb would fill the VST and get it to run well for a short time before it ran out of enough fuel.
But I think throwing parts at it and hoping is not a good way to trouble shoot your motor.
if you cannot test it properly then find someone that can.
Having a service manual for your motor helps a lot

[panasonic]

Seeing it started soon after maintenance, filters ect. Check water separator filter gasket and flange where filter gasket seats. It can suck air there and cause the symptoms you describe.

Fixed my cousins F60 last year doing exact same thing right after filter change. He bought cheap filter off Amazon and gasket would not seal...put Yamaha filter on it and zoom, zoom.

Filter did not leak fuel but sucked air. Something to check.

[panasonic]

Fuel may very well be on it's way out, but many things to check first as 99Yam40 already said. Fuel pumps are not cheap and don't fail very often. Good luck and report back your progress please.