92 GTX has me stumped

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Hi guys long time lurker but I cant think of anything else at this point and I'm open to suggestions,

Short backstory:
A couple months ago I picked up a 1992 GTX for cheap. Its in good condition the PO was parting with it because it would run but not shut off with the lanyard or off kill button. Easy enough so I swapped out the MPEM and problem fixed and it ran great. After the maiden ride however it lost power and died on the way back to the dock which I thought was odd but ok so back to diagnosing issues and there is nothing coming out of the coil even though it is getting signal. Ok so I replace the coil and we are back in business and running great again. Had it out for a weekend at a buddies cabin and the first day it ran great all day no issues but the second day it was very hard to start but I eventually got it then proceeded to suck up a ski rope immediately... managed to cut that out and got it back in the water and was running good again until my buddy came back and said hit a wave and it died in the middle of the lake. He was able to fire it up and idle back but it sounds like its running on one cylinder or a bad misfire or something.

So when I got it out of the water I noticed a couple motor mounts busted so I thought maybe the pump was getting hung up because of misalignment and making it run rough so I replaced all the motor mounts and made sure the engine and pump spin freely. There was also more than a usual amount of water in the hull which I contributed to sucking up that rope and getting it wrapped up between hull and shaft. Anyways, went to fire it up and still it sounds like its running on one cylinder or misfiring I cant really tell and wont rev at all and barely holds this rough "idle".

So far I have checked that it has spark, good compression, seems to be getting fuel (plugs wet), carbs are clean, rotary valve gear isn't stripped so I don't see how the actual valve plate could've moved. I really just don't know what else to check from here. I don't think the problem is internal to the engine and I'm hoping I don't have to pull it out.

Sorry for the wall of text any suggestions welcomed
The simple basics of a '92 ski are good battery and good fuel delivery. You say the "carbs are clean", but you have no idea of their internal condition (I assume). When was the last time (if ever) that the carbs were rebuilt?, does the ski still have all the stock fuel hoses (grey ones?).....

The basic rules of thumb on older vintage skis -> replace all fuel hoses (grey to black), replace fuel selector switch, replace fuel filter O-ring, rebuild the carbs. If the compression is still good (what are the numbers BTW?) and IF it was only running on one cylinder the compression would be lost on the non-operable one (so it's probably not that).

I'd start with all that and see where it takes you and the ski. Rebuild the carbs with ONLY GENUINE Mikuni parts (all other carb aftermarket stuff is a fools errand - trust the collective wisdom of the forum on that, at least).
I took apart the carbs and they are very clean inside and all the seals look good along with the Jets are not blocked. I haven't rebuilt it but nothing seems out of place to make it run as bad as it is.

Both cylinders have 150psi and all the fuel line has been replaced already. This is why I'm stuck haha.

Is there a way it could be electrical even though it is getting good spark? I could look into a carb rebuild kit as well.
Did you happen to get it running? You didn’t mention the little screen in the carb. I’ve had those gummed up pretty bad. I’ve also cleaned out my carbs and everything look great but then would run weird and not right and after actually rebuilding they ran like scolded dogs.
Do you have an IN LINE filter on the ski? Those bastards wreak havoc and you won't find a problem.
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