WR250R does not start - Fault Code No. 12 Error - Crankshaft

Hello my name is Timo and I live in Germany, please bear with my English if something is wrong.

At the end of last year I had an engine failure with my Yamaha WR250R, because the alternator must have loosened from the crankshaft. Over the winter I had the engine rebuilt by a mechanic and installed it in my bike at the beginning of this year. When I turned on the ignition I got error code 12 (Crankshaft Position Sensor - CPS) on the dashboard and the check engine light started to come on. I found a few forum posts but nothing could help me so far.
When I try to start the bike, the starter doesn't turn and the cockpit shuts off or flickers until I release the start button. Also, there are "click?" noises from the tail, so probably from the starter relay. One at a time at first and now rather quickly one after the other.

I have already checked the following:
- started in neutral gear and in 1st gear with clutch pulled
- started in neutral gear and engaged 1st gear to move the crankshaft a bit
- connected another battery and tried to start with jump-start from my car via the bike-battery
- bypass the starter relay and then start it
- measured the resistance at the CPS-Coupler -> constant approx. 261 Ohm
- measured the resistance at the CPS pins on the ECU coupler -> constant approx. 610 Ohm
- clear the error code in the diagnostic mode

I have now ordered the gaskets for the alternator/generator cover and a matching starter relay from Arrowhead. Unfortunately, I can't buy the crankshaft position sensor separately - only the whole alternator stator.
Maybe someone has had the same problem or knows what else I could do.
Thanks in advance!

Did you talk to the engine builder about this problem? From what you say it seems that he missed something while rebuilding the engine.

johnkol wrote:

Did you talk to the engine builder about this problem? From what you say it seems that he missed something while rebuilding the engine.

Yes, he thinks it's the battery that's causing the problems. He can look at the problem directly only in a month, but I would not want to wait that long.

If he's not willing to look at a rebuild that he potentially screwed up for another month, then I would be really worried of him accusing you of creating the problem through your troubleshooting.

Didn't you tell him that you tried another battery and the problem was still there?

whatever was your outcome, I have almost the identical problem w/ no start meets code for crankshaft issue.

thanks.

The OP has not logged back in since his last post in this thread, so don't expect an answer anytime soon.

If bike has thrown Fault Code 12, troubleshooting is on Page 8-41 of the service manual; have you followed those steps?

johnkol wrote:

The OP has not logged back in since his last post in this thread, so don't expect an answer anytime soon.

If bike has thrown Fault Code 12, troubleshooting is on Page 8-41 of the service manual; have you followed those steps?

Hi, I've been attempting to help climberdimer with this issue. We both have 2008 WR250Rs.
I have the shop manual but trying to find information there is a challenge, at least for me. The info on troubleshooting isn't connected to useful location data. We have looked at and cleaned all the connectors in the area on both sides of the head tube. Have not been able to locate or ID the specific connector for the crank sensor (any hints appreciated). We have not yet pulled the side cover. The starter relay clicks loudly when the start button is pressed, that's all we can get out of it now. No other faults in the diagnostics.

The bike had an engine rebuild less than 500 miles ago. Stator recall work was also done within recent history by the same shop. We are wondering about that work and whether a wire got pinched. That shop is at least a month out to see the bike at their place. We can do the test on the sensor if we can find the proper wire for it -- it's the finding that we have so far not figured out.

AeroDork wrote:

Have not been able to locate or ID the specific connector for the crank sensor (any hints appreciated)

The location of the Crankshaft Position Sensor coupler is shown on Page 5-2; the information on how to check it is on Page 8-75.

I would also suggest you find a new mechanic; a bike fails 500 miles after an engine rebuild and the shop does not open its calendar to slot you in immediately?

johnkol wrote:

The location of the Crankshaft Position Sensor coupler is shown on Page 5-2; the information on how to check it is on Page 8-75.

I would also suggest you find a new mechanic; a bike fails 500 miles after an engine rebuild and the shop does not open its calendar to slot you in immediately?

Very helpful, thank you! I thought I was close, and I had that connector in my hands and checked/cleaned it but didn't know for sure it led to the right place. I didn't want to tear into the wiring of someone else's ride.

And yes, I agree, time for a new shop. Hoping we can get this figured out without involving them doing more work. My understanding is that the sensor is part of the stator assembly and it can't be replaced on its own. My buddy will have to negotiate with that shop and/or Yamaha to come up with a solution if the whole thing needs to be replaced.

Thank you again!

AeroDork wrote:

My understanding is that the sensor is part of the stator assembly and it can't be replaced on its own.

That is true; you mentioned that the same shop did the stator recall, so the CPS would have been replaced at that time. Maybe they did not properly torque it and it moved? Or the wires were not properly routed and one of them was severed?

johnkol wrote:

That is true; you mentioned that the same shop did the stator recall, so the CPS would have been replaced at that time. Maybe they did not properly torque it and it moved? Or the wires were not properly routed and one of them was severed?

Hoping to find out soon. We are weeks (or maybe months) out from riding weather so have some time. Definitely will post what we find out in case someone else stumbles through here with a similar issue. Thank you again for the replies and help.

AeroDork wrote:

johnkol wrote:

That is true; you mentioned that the same shop did the stator recall, so the CPS would have been replaced at that time. Maybe they did not properly torque it and it moved? Or the wires were not properly routed and one of them was severed?

Hoping to find out soon. We are weeks (or maybe months) out from riding weather so have some time. Definitely will post what we find out in case someone else stumbles through here with a similar issue. Thank you again for the replies and help.

Wrapping up this thread for my friend's issue...

He got it into the shop and they found a bad connection at the starter relay. Cleaned up and bike starts fine now. We missed what should have been an easy fix. Hopefully our lesson will be an easy solution for someone else out there.