GT40 Surging and Top End

When I first purchased my 95 after it had sat in a garage for nearly 20 years, (100 hours in 20 years) it had a similar issue.   It was winter and I had time to play so I changed the impeller on the water pump, I had seen some temp variation although no overheat. I changed the cooling temp sensor that sends information to the computer and the oil pressure sender that sends a signal to the computer, not the one that powers your oil pressure gauge. I changed the Fuel filter and tightened all the hose clamps on the raw water intake system from the boat bottom to the raw water pump to make sure it was not sucking air.   Also had to fix the seal in the water strainer.
Last I cleaned the connections on the lanyard that plugs into the gear shift /throttle control, this is the safety kill switch that can kill the engine if you pull it out. I just made sure it was clean and put a little electrical lube on the contacts.
Since I did all this at once and the problem has not come back in 2 years I know one of the above got me back running well. It has not missed a beat since.
I believe there is a thread on this site that addresses the GT 40 and common issues they have. Be worth it to read what it says.

I think you'll solve this quickly by doing proper troubleshooting and not tossing parts at it. Top speed of 35 with a GT40 and an Acme 644 should be at least 44-46. Take your time and verify each system. I'd look at fuel first. It seems a lot of us have found issues with the LPP and FCC. Get a pressure gauge and install it and eyeball it while running and watch for needle jumping.

You are correct. No FCC. LPP fuel pressure is something like 6psi but the pressure you're reading off of the Shrader valve is 40psi and steady. I don't know where you'd read LPP just never did it. I had massive variations at the Shrader so I replaced LPP and all was good in my case.