1996 GTX Surging and won't rev

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Lothsahn

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I have a 1996 GTX I just bought a few months ago.

The first time I took it on the lake, it ran great.
The second time I took it on the lake, it would only rev to around 4000-4500 RPM until it warmed up. Then it ran great.

I cleaned the rave valves, which were extremely dirty. In addition, one of them was cracked near the stem but no pieces got into the cylinder and I visually inspected the cylinders and didn't see any damage. Don't have a compression tester, but I know it was tested at 150 psi on each cylinder 2 years ago. Both rave valves are now replaced with new slotted OEM valves, cleaned passageways, and rebuilt bellows.

I took it back to the lake and it, again, ran very poorly until it warmed up. This time it wouldn't exceed 2500-3000 RPM. Once warmed up, it ran *great* for about 5 minutes (>45 MPH at around 2/3 throttle), at which point it suddenly lost power and went back to running poorly. It was again running 2500-3000 RPM and surging--not a constant low RPM. The more throttle I gave it, the harder it would surge. At idle, it was running smooth. I tried pulling the choke slowly while it was surging, which didn't seem to make any difference; however, pulling the choke all the way out did cause the engine to quit.

I put the seadoo back on the trailer, took it to my garage. I checked that the spark plug caps were both firmly attached and snug (they were). Boat also revs just fine out of water.

I then read that this can be caused by a failing rectifier. At 5k RPM, the rectifier was putting out more than 15V. (somewhere between 15 and 16v, increasing as I revved the engine). I saw here that more than 15V indicates the rectifier is bad:

Questions:
1) Would you agree that the rectifier is bad?
2) Why does a high voltage from a rectifier cause the seadoo to run badly? I would think overvoltage could damage the MPEM, but I don't understand how it would cause it to run rough. However, people say that pulling the red wire is a good way to check the rectifier. Does the MPEM cut ignition if there's too high voltage?
3) Anything else I should check? Keep in mind that I'm not super mechanically inclined, so I am missing a number of tools and skills that I need to test some things (for instance, I don't have a compression tester).
 
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