2001 SAN rough running under load

Wow great link.

Well I replaced plugs, cap, rotor fuel filter... Definitely smoothed everything out, however
when towing two people on kneeboards, definitely noticed a little more roughness or missing.

I plan on replacing plug wires and will look through the link on the GT40 issues.
link, which is great by the way.

GT40 in our 95 ski ran rough when we bought it. Only about 500 hours on it but you could tell it wasn't running right...wouldn't quite get up to max rpm, slow out of the hole etc.

We did cap, plugs, plug wires and it's like a new boat.

Is this a GT-40 motor?

Background: Picked up this 2001 SAN earlier this year, boat appears to be in good condition. Not sure how many hours on the boat because the gauges have been changed,

I checked fluids and we have ran it about ten times so far this year with no issues.
Not very long days mind you, 2-4 hour family sessions with riding, swimming etc.

Yesterday we were teaching our 13 year old how to drive and I thought he was having issues maintaining speed while i was riding, no biggie first time trying to pull someone.

I jump in the drivers seat and start his first run, I instantly notice increased vibration almost like it is missing at lower rpms. Also as i slowly add throttle it goes to this lumpy rough running engine to this smooth running engine that accelerates rapidly. The best way to describe it is it feels like getting on a pipe on a motorcycle or on cam on a car.

I end run immediately and start heading back towards the dock, it seems to occur less frequently when not under load?

Fuel gauge is at around 1/4 tank

Thoughts on where to start trouble shooting this issue?