Super Jet 90 SJ Issues

Just bought a modded 90 SN and took it out for the first ride of the season this past weekend. Rode for about 15 min before I realized I was running on one cylinder so we pulled it out of the water. When we got back home we took a look and one of the plug caps was partially disconnected. Reconnected that and checked to make sure I had spark in both cylinders. Spark was good and fuel was moving through the lines, so we cranked it again. It would turn over once then quit.

We pulled the ebox to make sure the heat sensor was disconnected, fuse is good, wiring looks good. Pulled the carb to check the fuel filter and that was clean too. Bypassed the fuel selector switch and ran fuel line straight to the carb, still wouldn't stay running. Any ideas? I'm running out of places to look.
 
head gasket?
if you ran on one cylinder you could have internal issues,

do a compression check and make sure both cylinders are even.

or you can pull the head to inspect but you'll need a new gasket.

if you are getting good spark, not sure why you would have gone through the e-box. and you know one cyl is getting fuel, provided your intake manfold has the cross over, it's a safe bet both are getting fuel so issues could be internal.

what is your cooling system like? bypass spitters?
when you run the motor dry are you getting exhaust blow back through the cooling bypass spitters? this would be a sign of a bad head-gasket depending on cooling routes.
 
It never ran good at all? Just sounded like it bogged the entire time and one cyclinder was hot and other luke warm? 15 minutes is an forever when my ski is running on one cyclinder, I can barely make it on plane..
 
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