Put in new spark plugs. Id recommend ngk br8es. Run wide open throttle for atleast 30 seconds. Do not let off throttle but pull lanyard to kill engine. Pull plugs and see what they look like. Whether rich or lean. Of course do in a safe environment.
Are you going off of factory tach for rpm? My 97 gsx only turns about 6700ish. You maybe searching for a ghost. If it were mine, i would lower the pop off pressure and run it. I only say that because ive seen high pop off readings that are still in spec to cause bogging issues.
Congratulations on owning one of the most awesome seadoos ever, (Imo). Have you checked the clmpression? The fuel systems on these older 2 strokes always need to be up to par. The carburetors and fuel system is always a good start. Especially if it hasnt been gone through in a while. The fuel...