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1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

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  • 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

    Hey guys, I bought a boat a while back with a 1989 Yamaha 40hp 2 stroke, 3 cylinder that I've been raking my brains over trying to get it running right. Initially it had sat up for a couple years, so I went through the carburetors with a new rebuild kit (about 4 times now), replaced the fuel filters and cleared out the lines, pulled and capped the oil injection system (I'm running premix now), changed the plugs, and pulled the powerhead and replaced the lower crack seals and the gasket between the powerhead and middle shaft.

    It will basically run like a charm for the first 15-20 seconds when you first crank it, but right after 15-20 seconds, it will begin to spit and sputter and die out. I bumped up the timing enough so that it will run like this, but you can tell it's only on 2 cylinders of the 3. I have narrowed the problem down to the bottom cylinder because you can pull that plug while it's running and it makes no difference to its tone. When you pull the middle or top plug, the motor will die. The bottom plug also looks a little cleaner to where it doesn't seem to be burning right. You can see the bottom cylinder is getting spark, so it shouldn't be the coil. I pulled the CDI Mitsubishi timing box module thing and went through the wires to make sure all the connections were good and it all checked out.

    I ran it on the water a week ago, and it did the same thing. When you first crank it, it will run like a dream until about 15 or 20 seconds and it will start to die out (it starts running on 2 cyl). I also noticed that if you do a hole shot and floor it, it will kick up and throw you out of your seat (definitely on all 3 cylinders), but after about 3 seconds it will die back down. It seems that at certain points or situations it sends correct spark to the bottom cylinder, but other times it doesn't to where the bottom cylinder isn't firing right or making power. When you open up wide open, it will go but it spits and sputters and doesn't move very quickly, so it definitely is running on the top 2 cylinders only.

    I just wanted to check with you guys and get your opinion. My last resort is to replace the CDI unit since I figure it isn't sending correct spark to the bottom cylinder, therefore causing all the problems I mention. It doesn't seem to have any damage or corrosion or anything (the entire motor actually looks like new under the cover). So, should I spend $400 on that darned CDI box, or is there anything else I can try? Also, does anyone know of a cheaper solution; can I send the CDI box to some place for repair at a lower cost? Thanks in advance!

    Edit: I forgot to mention, but the compression in all 3 cylinders is spot on and I did a leak down test and it is almost literally perfect. It doesn't seem to knock or make noises, so it shouldn't be anything internal.

  • #2
    Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

    Intremitent CDI failure for the 3 cylinders is not uncommon. The last time I talked to Rapair or I think they are now CDI electronics, they were making a replacement for it.
    I think I may have a used one which was working fine when the motor croaked from lack of water pressure.
    E mail me at neudecray@hotmail.com and I will look and see.


    • #3
      Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

      Thanks for the info, I sent you an e-mail.


      • #4
        Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

        start testing the components


        • #5
          Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

          The 15-20 seconds thing is normal. Initially the CDI seems to advance and then die back to idle. The CDI's job is just to send a spark so if you think it is not sending one to the 3rd cylinder you can attach a timing light and see if it stops sending. Certainly you need all three cylinders to throw you out of your seat but dying after 3 seconds could suggest a fuel issue.


          • #6
            Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

            Well, I ended up ordering a new CDI so we will see what happens. Is there anything else worth replacing at the same time? I was going to order the coils but I think they were about $60 a pop, so I passed on that offer. I'll let you guys know what happens after I get the new CDI in.


            • #7
              Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

              your most likly going to have a spare CDI box.
              a better way to test it would simply check the primary coil voltage at all 3 coils to see if one is missing an input.
              next best would simply be to index the flywheel for cylinders 2 and 3 and simply run a timing light and insure the correct plug was firing.
              some of the 3 cylinders ran a box with a TPS inside that was driven from a rod on the throttle linkage.
              other old ones had 3 pulser coils and CDI failures were rare.
              in 12 years or so of playing with yamaha I may have seen 2 bad coils, and maybe 5 bad CDI/ECU failures.
              its just rare.
              thats why proper testing is so mandatory
              no tech questions by PM, they wont get answered.
              you have to be trusted by the people that you lie to .


              • #8
                Johnson 75 problems

                First the engine was stuck in reverse. Then I got the tilt and trim to pick the engine up to see WTF was going on. Tilt and trim stuck up all the way. Filled up the oil reservoir on it. Think the rings are going bad in it.
                It's still stuck in reverse. Took control panel off and cleaned up the junk in there. Lever works somewhat better, but still something is wrong. Still stuck.
                Any help appreciated.
                Just got this boat last month....


                • #9
                  Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

                  Unfortunately, he does have the model with the tps built into the CDI box. The most likely to fail and the hardest to trouble shoot when they are intermittent.


                  • #10
                    Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

                    yep, thats why the test wheel,flywheel indexing and a CD77 are so important.
                    I have also found if the pointer on the CDI goes past the mark it will create isues.
                    but the nedle will deflect rapidly at coil misfire on a CD77 that a digital meter may or may not see. the timing lamp with the flywheel indexed will show if a cylinder disapears or fires at an incorrect time.
                    but the test wheel is about mandatory.
                    no tech questions by PM, they wont get answered.
                    you have to be trusted by the people that you lie to .


                    • #11
                      Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

                      I didn't see anything about shooting a little fuel into #3 carb to see if it picks up RPM again. Quick & easy test to discern if it's carb or electrical. I'd also reattach the O/I lines, or remove the entire system-drive gear and all, and install a cover plate. When that drive gear runs too long without lube it'll lock up and destroy most of the bottom of the crank. You may also want to make sure you installed the bottom crank seal in the proper direction, as you could be blowing fuel out there instead of drawing it through to the combustion chamber. As far as stuck in reverse, disconnect the control cable from the shift at the engine and see if you can then select gears manually moving the shifter on the engine. If not, check where the shift rod connects just above the lower unit. Water may have eroded it util it won't swivel the gearcase part of the shift rod. Don't you just love boating?


                      • #12
                        HELP Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...H E L P

                        Getting Desparate

                        SuB8HaVeN maybe you can help as it seems you are little further down the road than I am. I need help identifying the part numbers I need.

                        I made the mistake of buying a:
                        Late 80's Yamaha 40 hp Enduro
                        It fell in the river and the CDI appears shot, maybe coil as well.
                        The part number on the Mitsubishi CDI reads (in 3 lines):
                        of course no one in the US can cross-reference it.
                        Any potential info you can share regarding model numbers, serial numbers, codes, or part numbers would be greatly appreciated.
                        What is the part number on you CDI?

                        Unfortunately, the plate is gone so I do not have the exact model number or serial number. I dont even know the exact year.
                        Here is some of the "possible" info for it
                        Late 80s early 90
                        Possible model number: 6J4 1984- 40JM
                        The 6J4 was made 1984 onward
                        Code 6J4
                        Model 40JM
                        A sample late 80s Enduro Serial number:is: 6J4-S-010565
                        Addition model numbers are:
                        267080, 267081, 267082, 267200, 267201, 267211


                        • #13
                          Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

                          does anyone no were i can get a cheap crankshaft for a early 1990's 40hp yamaha 3cyl..thank you


                          • #14
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                            Re: 1989 Yamaha 40hp 2 stroke 3 cyl CDI issues...

                            Does anyone know if 1989 40 hp Yamaha controls can be used with any other make of motor ?