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New Islandia owner trying to get through some engine problems

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fvcoachv

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Good morning guys. I have a 2000 Sea doo Islandia with the 240hp m2 jet drive. I bought it a month ago and the guy had rebuilt the engine, put new interior, and did lots of little things. However, he seemed to have pulled every fuel, oil, and wiring harness. I have had a great time putting in the hydro turf, got a great deal on a double bimini, stereo/speakers, and getting the mercury and sea doo manuals. I love the Islandias and have wanted one of these since they came out. Needless to say, I was excited to finally get one.
After a month, thought we had everything back in order (or so I thought). The engine started up fine out of the water with the hose connected. So we took it out on the water last weekend. It was very hard to start but got going after several attempts. It was fine for about 20 minutes then shut off. We could not get it started again. Now after clearing filters and time, we are now able to get it started but now there is a scary low knocking noise. It gets throttle and stays running but some of the cylinders seem to be firing and some not. So here is the question. Is there a chance the knocking noise could be anything other than a major fix like a thrown rod or sized piston? Could there fuel line or related issues causing the knocking noise? I just want to check the easy things before spending the big dollars on another rebuild. I live in Huntington Beach and have not found any local guys who work on the m2. Thanks for any advice and here are some of the pics of how it has been coming along on the cosmetic side so far.
IMAG0056.jpgIMAG0063.jpgIMAG0062.jpgIMAG0066.jpg
 
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