1999 GT40 sputters out then restarts

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  • Moomba99
    • Jul 2026
    • 5

    • Granbury, TX

    • 1999 Moomba Mobius

    #1

    1999 GT40 sputters out then restarts

    Last year after having some work done on my boat, including replacing both fuel pumps and throttlebody, I boat ran great for about an hour and a half and then it sputtered out. It cranked right back up but has continued to sputter out on an increasingly frequent basis. It currently sputters out every 2 to 4 minutes, but I’ll give it a few seconds then fires right back up. I took it in earlier this summer and they identified the issue as a faulty low pressure pump (non-OEM) that was installed last year and bad fuel. I filled it up with ethanol free but I’m still having the same issue.

    We took it out yesterday and ran it on a portable tank to confirm that the issue is engine-side. Fuel pressure is only reading 35 psi and then quickly drops to 0 when sputtering out. If we give it a few seconds it cranks right back up but generally, we can’t run it as hard for as long before the issue happens again. There’s only been one situation where it wouldn’t start back up and I couldn’t get back to the house.

    im going to try to remove the FCC cover later today to further investigate.

    I’ll also mention that we replaced the MDC computer a few years ago.

    Any initial thoughts on whether the problem sounds electrical, computer related, or pump related?
  • Moomba99
    • Jul 2026
    • 5

    • Granbury, TX

    • 1999 Moomba Mobius

    #2
    Update: I drained and out the FCC. There was some sand and sediment. I confirmed there’s a Walbro HPP installed. I replaced the filter.

    this morning the boat ran well for 15 minutes at about 15 mph. The we ran short ski and tubing sessions a for about 36 engine hours before the issue happened again. Boat sputtered out. I tired to restart and it quit as I shifted into gear. I waited 5 minutes and was able to start the boat up and make it back to the dock.

    Comment

    • Rednucleus
      • Jul 2022
      • 250

      • WA

      • Club Boat 2014 Ski Nautique 200

      #3
      Sounds like something is failing when it gets hot - electrical is my guess - fuel pump relay?? I assume this was not happening before you did the work last year??

      Comment

      • SilentSeven
        1,000 Post Club Member
        • Feb 2014
        • 2200

        • Bellevue WA

        • 2004 Nautique 206

        #4
        Take a close look at your distributor. I had some run problems - different from yours - that turned out to be a flakey hall sensor. Replaced the distributor with a remanufactured automotive unit and my problems cleaned up.

        https://www.planetnautique.com/vb5/f...e-replacements

        https://www.planetnautique.com/vb5/f...445#post345445

        https://www.planetnautique.com/vb5/f...le=#post345989
        2004 206 Air Nautique Limited - Black with Vapor Blue (family style)
        1997 Masters Edition Nautique - Zephyr Green - gone (amazing ski wake)
        1982 Mastercraft Powerslot - gone (a primitive but wonderful beast)
        Bellevue WA

        Comment

        • Jonny Quest
          Senior Member of PLANETNAUTIQUE
          • Aug 2014
          • 449

          • Salt Lake City, Utah via Texas

          • 2003 Ski Nautique 206 Limited with ZR6 Engine

          #5
          Closely examine the short fuel line inside the FCC that goes to the HP pump. Those have been known to crack and cause similar symptoms. It's an easy fix...

          JQ

          Comment

          • Moomba99
            • Jul 2026
            • 5

            • Granbury, TX

            • 1999 Moomba Mobius

            #6
            Thanks Jonny. That appears to be atleast part of the problem. I removed the FCC to inspect the high-pressure pump. it doesn’t appear to have been installed with a submersible fuel line, the fuel line appears to be too long, and I don’t think they used the right clamps.

            Comment

            • Moomba99
              • Jul 2026
              • 5

              • Granbury, TX

              • 1999 Moomba Mobius

              #7
              Update: I drained the FCC and replaced the filter. There was some sediment and sand that I needed to clean out. Performance improved, but I was still seen the issue under sustained the load. I confirmed that Power wasn’t dropping out, and the HPP had been installed with a fuel line that did not appear to be submersible spec grade and was too long So the HPP was kind of getting smashed inside the filter. I replaced the fuel line and the HPP to be safe and so far so good

              Comment

              • Moomba99
                • Jul 2026
                • 5

                • Granbury, TX

                • 1999 Moomba Mobius

                #8
                Update: I drained the FCC and replaced the filter. There was some sediment and sand that I needed to clean out. Performance improved, but I was still seen the issue under sustained the load. I confirmed that Power wasn’t dropping out, and the HPP had been installed with a fuel line that did not appear to be submersible spec grade and was too long So the HPP was kind of getting smashed inside the filter. I replaced the fuel line and the HPP to be safe and so far so good

                Comment

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