Engine not getting enough air

I have a 1985 Ski Nautique 2001 with a PCM 351 in it. Yesterday, the boat was running fine for the first set that we did and then in the middle of the second set the motor acted like it wasn’t getting enough air but then it recovered. Eventually, the motor died and you would be able to start it w/o opening the engine cover. We made it back to the beach and I checked the hoses from the bow and everything looked normal. I then started it with the engine cover down and it ran fine while not moving. Tried to take it out again but had the same air problems once it got moving. As long as the motor cover was up or not moving it ran fine. Does anyone have any ideas?

Thanks, Blake

The reason that I am pretty sure it is a air problem is because when it died while we were still on the lake it wouldn't completely turn over and stay running for a period of time, but when I would raise the engine cover it would fire right up and stay running. I made it back to the beach and checked the hoses in the bow and everything looked normal. I then fired it up with the engine cover on and off and it idled there for 10 minutes or so. After a while I decided to take it out again to test it and it started to hesitate and die but I lifted the engine cover before it did and held it open until we got to the beach and it didn’t die as it was getting more air. That is why I believe it is an air flow problem.