I blew a head gasket on my 00 em1 so i replaced the head gasket, timing belt/water pump, replaced cam seals, intake gasket (old one was leaking), and changed oil/ flushed radiator. After everything was back together started up fine, but is idling a little high. Let it run for 10 mins and it purred like a kitten. Went to back out of driveway and CEL started flashing and a clicking noise started coming from passenger side of the car. Checked fuse for ECU and it is fine. Here is a video of what it's doing. Thanks in advance!

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Flashing ECU indicates misfire, but your ecu is flashing too erratically. Check the codes. Also this can happen with the main relay is clicking on and off, the engine will stumble as yours does. Check the ground on the engine thermostat housing and clean it as necessary. Perhaps try swapping the main relay with a known working one and see if there is any difference.

 

Sorry forgot to mention, the only code it is throwing is 65, but I don't think that would have anything to do with this. Then again, I could be wrong.

 

Check your grounds (even your negative battery cable)! I've got a feeling it is your main relay clicking and not the ECU.

And it is unlikely that that code has anything to do with your problem.

 

You need to check your grounds especially the thermostat ground and also your battery grounds and power cable on the battery.

 

http://www.youtube.com/watch?v=Ip5i6...layer_embedded

 

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