2003 GTI cutting out on water and having trouble starting back after

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Got a 2003 Seadoo GTI LE RFI from a friends family who had purchased new ones. It had undetermined issues, but had been garage kept whole out of the water and is physically in great shape. Recently installed a reman engine from SES. Also replaced the starter and starter relay, coolant temp sensor, put in a new battery, and checked all the fuses. It fired right up on the trailer, I let it run about 30 seconds each time and it seemed great.

Took it to the lake for the first time today and it was idling a little rough, but seemed ok at first. But then, after only a few minutes (3-4) it cut out and was difficult to start again. It did this several times, and became more and more difficult to start again. We never got it past 3,200 rpm, (but also wasn’t trying to take it too high because it was the first time out with the reman engine). It didn’t seem to be cutting out at any particular rpm though, it just happened randomly- sometimes while idling in the no wake, sometimes while reving.

Thought it may be the battery, so put it back on the trailer and drove to the marina for a replacement. Put it back in the water and it continued to have the same problem.

Once out of the water it still starts up perfectly and sounds great.

The display is also not showing the speed (digital readout nor the dial), nor the hours (it just shows dashes where the hours should be).

Any thoughts on remedying this and getting it running? Thanks!
I have this same kind of problem on my 717 gti le -02 atm. I noticed it wasn't chargin the battery at all so I started from fixing that problem first. I also ordered a new carburator build-kit so if it doesn't fix with new stator, regulator etc. I'll build up the carb too :D
Sounds like a fuel issue. Did you change the fuel filters?
mikidymac i have not done anything to the fuel system yet shy of draining out the old gas and filling it up with new (as well as the oil tank)

I am thinking my pump might be failing, maybe it is able to provide enough gas to start up after a few seconds of turning over but not enough to sustain the engine? I was thinking about pulling the fuel pump, fuel regulator and injectors. Any recommendations on which to start with first? I am also experiencing low RPM, in the range of 1200 when on the trailer, so i know this is a real problem. Is there anything i can do without having a candoo or MPEM programmer? From what I can tell there is little manual adjustments that can be done on the throttle.

Another possibility i have been considering is that there is an issue with the DESS, if i am getting an intermittent signal due to a poor connection or failing sensor that could certainly be a cause.
so I replaced the fuel filters, they were really dirty so I know that was a problem. However on the trailer it is still idling around 1500 rpm, is there anything I can do without the Seadoo MPEM programmer? I plan to take it out again tomorrow but in all reality I expect it will keep cutting out.
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