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99 Seadoo GSX Limited won't crank/no spark

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My friend bought a 1999 seadoo GSX Limited 951 ski missing a few pieces. The seller stated that it needed another MPEM due to this one not even communicating with his Key Programmer/Tester. After collecting missing parts such as piece of exhaust, throttle cable with TPS and assembling, the ski will not crank as if no electrical power.( We are both very mechanical, a lot of automotive experience, and I have experience with my own 2 99 XP 951's). I did make the mistake of placing the MPEM (both) on my 99 XP to verify they worked (fried some of my wires in my coil box that I am fixing-likely my stator too), but both the ebay & original MPEM will start and run my ski (acts like timing is way off and back fired) in identical fashion. In other words, they recognize their lanyards and provide power to starter and ignition system.
So far we have done:
1) Replaced MPEM from a pwc recycler (ebay) that stated it was from a good running ski.
2) Tested each wire in the entire harness with a Mulimeter to confirm good continuity.
3) Installed new fully charged battery, drained F tank & added new fuel, drained, cleaned and added new 2 cycle oil, rebuilt carbs with new kits
4) Tested with multimeter, the stator & pickup.
5) tried disconnecting temp sensor & oil level sender from harness
6) Verified all Fuses are good
7) Removed and cleaned stator cover grounds (all 3 are under 1 bolt)
8) every connection on the harness was disconnected when testing harness and reconnected.
9) engine cranks when solenoid is jumped.
10) no power to solenoid "trigger" wire when start button is pressed.
11) round Multi-function Gauge is sun burnt badly, there is no way to tell if it is powering up or displaying anything.
12) pressing start button about 4 times (approx) the beeper will responed with a quick chirp with low volume tone, then another longer chirp with a louder tone, pressing button again gives two beeps of the louder tone. This seems the same on both the original MPEM and the ebay unit.
13) DESS post was replaced with a known working used one that was taken from my XP when I replaced both of mine a month ago.

There is no beeps when placing the lanyard on the DESS post.
Will a bad Multifunction display cause an issue like this and does it need to be connected and working for the ski to run? We tried disconnecting the front harnes for the gauges from the MPEM with no change in symptoms.
Also, will a 1998 MPEM work on 1999 model? I see the part numbers are different:
1998 GSX Limited Electronic Module Part#278001343
1999 GSX Limited Electronic Module Part#278001398
Anyone have the magic answer?
 
So we are making progress. We found the connectors within the harness connector that makes the electrical contact with the MPEM pins are not making proper contact by pressing and kinda twisting the wiring entering at the MPEM. We removed the 3 wires connected to the lanyard pin and gently pressed in the contact that actually touch the mpem pins and place back into pins. We now are getting the Double Beep from the lanyard and the engine now cranks over. We have no spark but we're making headway. We will do this to other pins to ensure they are making proper contact.
 
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We completed the rest of the pins. We also learned that the 98 GSX Limited has a single coil ignition where as the 99 GSX Limited uses two, and thus the MPEMs are not interchangeable. After doing the pins we got fire. The engine fired up on the 99 MPEM but didn't run well and back fired so loud it shock the crap out us lol! Obviously the timing wasn't right. After contemplating, we figured that the previous owner probably replaced the engine with a 98 and thus the flywheel was a 98. We purchased the 99 flywheel and sure enough, there was quite a bit of difference in the "triggering" blocks on the outer side of the flywheels. We swapped them, and found the one coil was firing strong but the 2nd one was very very weak. Even though both ohm'd out correctly, one was bad. We replaced the coil and now she lives! Timing sounds great, engine revs fast and strong as it should! Just a few more tid bits and off to the lake for a test run!
 
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Good news with the build is great to see, thanks for filling us in on the thread. I will keep that in mind for my own builds when i have to ferrit out electrical/ timing issues, good thinking there.

Cheers
 
Great troubleshooting. You guys are thorough !! Hope she hauls azz when you get it in the water!
 
The ski ran awesome after all this :)

We bought & fixed a few more skis and it was surprising that a couple of them also had loose/bad pin connections as well. This issue maybe happening to other folks more often than we realize. We now keep this very front of our minds when troubleshooting electrical.
 
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