2000 Ski Nautique Throttle Issues

I have a 2000 SN with the GT-40 engine. Today I had an issue with throttle/engine that I'm trying to narrow down before I start replacing parts. The boat ran well with no issues for 3 sets of slalom and then on the 4th set starting misbehaving. These are the symptoms.

1) Very slow hole shot and then getting up to course speed. It was taking the boat 5-10 seconds to drag me out of the water and then another 10 seconds to get to course speed. We tried disengaging perfect pass and controlling the throttle by hand to make sure that perfect pass wasn't the issue and the problem remained.

2) Significant hesitation of the engine when traveling at course speed. It would suddenly lose and then regain throttle within a second, sometimes several times within a second. The problem seemed to be worse at 36 MPH vs 34.2 MPH. The speed didn't change much and the hesitant wasn't major, but it was noticeable. We disengaged perfect pass and this issue also persisted. I observed the perfect pass throttle control directly to make sure it wasn't actuating.

Things we've checked or done so far:

1) Checked propeller (good)
2) Checked transmission fluid (good)
3) Checked engine oil (good)
4) Restarted the boat several times (no effect)

Is there anything common that might be causing these behaviors that I can look into first? Any rational order I should test solutions to cost effectively solve the problem? I greatly appreciate any help!

P.S. The boat had half a tank of gas and a friend is insisting that I may have water in the gas due to condensation overnight and I need to use STP. This doesn't seem quite right to me, but I'll try anything. Thanks!

When was the fuel filter replaced

Yes We do it every year. Check for water in filter can. Pump could be getting weak. Need to check fuel presser.

Also, I would add "GT-40" in the title of this thread. You'll be more likely to get some of the gurus to weigh in.