Intermittent Vibration/Shudder

Newbie here and I love the site. Just bought a '94 Nautique with the 5.8L. Took it out last week-end and put about 3 hours on it. Loved it. But Towards the end of the last day we had some intermitent vibration/shudder I'd like some help understanding. It went like this:

-AFter a great weekend of skiing, we push off from shore for one last run and pull up skier #1. At about 2000 rpm and higher, we notice that the boat vibrates and shudders, loses power but we can't really feel vibrations at low speed/rpm.
-Pull the skier in the boat, push the throttle down and we get the same vibration.
-convinced we must have somehow bent the prop/shaft when we pushed off from shore, we idle for about 5 minutes back to homebase
-Before docking, I figure: Let's try it one more time to see if we still get the vibes. We punch it up to speed but this time, everything is fine- no viration. We figure that we must have had something stuck on the prop that put it out of balance.
-So, Put Skier 1 back in and pull for 2 runs. All's good.
-Pull Skier #2 and do a run- everythings fine.
-Pull Skier #3 up and get the same shudder so we pulled him back in the boat.
-Punch it and of course, everythings fine, no shudder/vibration.

I tried to replicate the vibration again doing about 6 more stop/starts to no avail- couldn't do it. 0 to 45 with no problems. (In fact, it perfoms and sounds beautiful when not vibrating)

I did a search of the forum here and didn't find anything. I read the piece on alignment but it doesn't sound like those issues are intermittent? I called a local marina and the mechanic suggested that it may be a prop that needs tightening. Called the previous owner (whom I trust) and he says that he never experienced it. The engine has less than 500 hours on it.

Not sure when we will get the boat back in the water and it is stored about a half hour from our house. The intermittent nature of the problem is particularly baffling. (Three hours of greatness and about 30 seconds of "Holy Crap what is that?") Also, of the 3 times it did it, it did it twice while trying to pull a skier out and once with no skier. I'd appreciate any input and expertise on this board about possible causes.

Thanks guys.

GL,
The intermittent nature of the vibration could be the prop being loose on the taper and then tightening up again. Check it out and take a look at proper prop installation

Beyond that, I'm wondering about the engine missing at times? When it vibrates, is there any loss in performance?