It was having trouble idling in the water (but not on the hose) and would bog down when given throttle. Also has ~120 psi in each cylinder.
Was hoping the engine would make it through the summer and plan on rebuilding it next winter as I don't really want or have time to take on a project that big right now.
Obviously you already know 120psi is low. I have to wonder though since both are approximately the same, if your compression gauge reading is accurately calibrated (a common concern that needs to be confirmed before throwing money at a problem that doesn't exist).
If it won't idle well and hesitates at low speed this suggests the low speed passages are at least partially blocked with fuel gum and possibly aluminum corrosion and debris, so pay particular attention to cleaning the low speed "bypass holes" circled in yellow of the drawing I posted. These are either two or three holes in the carburetor bore just upstream of the butterfly critical for providing fuel during low speed throttle butterfly positions. Shooting acetone carburetor cleaner or brake cleaner under pressure through the brass pilot jet will remove the fuel gum and clear these passages most of the time, you can watch inside the bore as the liquid solvent shoots out from these passages inside the carburetor bore, it should produce a straight stream, not a trickle. A weak trickle or an angled stream indicates a partially clogged passage.
Occasionally, not just fuel gum but internal oxidation of the machined aluminum passage, corrosion can grow inside those "bypass holes" and cause partial blockage, or bits of fuel debris can become lodged in them and block fuel delivery during low speed operation. Often just pushing a piece of monofilament fishing line through them can clear them out if the carburetor solvent doesn't do the trick. Or in extreme cases very carefully using a fine piece of wire, but go easy so as not to damage the hole or scratch the inside, the size of the hole is drilled to a specific dimension and scratching the inside of the channel (or corrosion) can change the calibration. The bypass holes diameter is critical for low speed off idle operation, just as the orifice size of the pilot low speed jet.
The accelerator pump gives a mechanical shot of fuel as you open the throttle, this mechanically richens the fuel mixture briefly until air velocity through the carburetor bore can increase, and begin pulling fuel from the metering chamber through the bypass holes. So if the accelerator pump system (pump, and nozzles) isn't functioning properly, you are likely to experience a lean hesitation when applying throttle, from off idle. For instance, one of the accelerator fuel nozzles might be clogged with debris or fuel gum. Usually a few shots of carburetor cleaner passing through can clear them out. These nozzles have a check ball and spring inside them thus will only pass fuel inward, toward the inside bore of the carburetor, so check this, if they are operating correctly the fuel can only move in one direction. If one or both of them are clogged, then the mechanical fuel enrichment won't operate correctly and the result will be a lean hesitation when APPLYING throttle at low speeds.
If your lean hesitation occurs shortly AFTER this brief accelerator shot is consumed (engine begins to accelerate then falls on it's face), the problem is most likely due to inadequate fuel arriving to the inside of the carburetor bore (throat) which is normally delivered via the bypass holes.
Anyway, the yellow portions circled in the Mikuni owners manual drawing posted above are typical places where fuel debris tends to collect, note these locations happen to be the smallest passages inside the carburetor.
The red circle represents the needle and seat, the rubber tip of the needle tends to wear out or may have a groove that forms over time that can cause the needle to stick in the seat orifice. This makes for inconsistent air/fuel mixture ratios at low speed and can cause hard starting due to fuel leaking into the carburetor bore.
Think of this diaphragm type carburetor in terms of a fuel on demand system, where engine intake vacuum dictates how and when fuel is delivered via the configuration and diameter of the various passages.
Here is a link to the Mikuni owners manual, much of it is useful for identifying OEM parts numbers. You will need to make sure to use the correct parts for your application, some of which is provided in the seadoo factory service manual for your particular engine. It's vitally important to install only the correct parts else the calibration will be changed. These carbs were used on many different engines of various sizes and applications, so there were numerous changes in calibrated components depending on the particular application.
So, don't install the wrong components, double check that any parts used are the correct ones! Don't assume any part from your kit is correct, verify 100%, 1st.
http://www.mikuni.com/pdf/sbn_manual.pdf