Bill, I think your on to something however, my experience with this particular model points to a different but related culprit. The intake tunnel is a large one piece insert that is sealed to the hull with a foam packing type seal. If this seal is disturbed or breached the boat will react much as you've described and usually can't even be finessed to plane. You'll have to remove the pump and this tunnel to replace that seal. The fiche is a bit confusing on the required qty. You need to order 2 pieces of this foam packing seal. Good luck.
I would consider the potential culprit to be a blown head gasket. The missing cylinder hints at a blown gasket.
I think the messed up stators could be doing it. I had a similar experience on a 94 spi.
star chekin the comprecion if les and 135 psi or not even opend the head check for a leak in a gasket check the cilinder make sure is not marcs or scrach if the compresion is ok check for craks on the tunel of the wather intaque included the impeler housing if that is ok make sure the impeler is the recomended for you engine
my 92 waverunner III needed teh internal filter to be cleaned on the carb.. wouldnt get out of its own way.. even if thats not the problem.. couldnt hurt.. and might as well rebuild the carb while you have it off