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Has anyone successfully used a drz400s motor and cdi with a drz400e wiring harness?

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I have a 2004 drz400s motor and cdi that I put into a drz400e frame and wiring harness. This motor ran before I switched frames and harnesses but now I can't get it to start. 

I grounded the black wire with the yellow stripe coming from the cdi so I have spark now. The clutch switch is bypassed, the neutral switch coming from the motor is not connected to anything, and there is no kickstand switch (I believe that's why you ground the black/yellow wire). 

When I press the start button it turns over but never catches. It's made a loud "pop" from the muffler a few times.

Jetting, muffler, intake are all stock (minus k&n air filter). I've rebuilt the carb and still nothing. I even tried putting the carb, starter coil, and spark plug wire from my other 400s (which runs great) and still nothing. 

Where do I go from here? Electrical? Valve clearance? I checked the timing, it's good. Any help would be appreciated!

 

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I believe there is a slight difference on the Ignition box between the E and the S. Should be documented somewhere on this BB.

As always, when an engine doesn't start, but is good mechanically, hit it with a shot of starting fluid. If it doesn't fire up, you need to troubleshoot your ignition.

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How do I trouble shoot my ignition? So far I have replaced the spark plug, starter coil, spark plug wire... I even tried using the E cdi with the harness set up normally. I also put this S cdi in my other bike to make sure it would start up. 

I checked my valve clearance and my exhaust is at 0.178 (spec is 0.2-0.3mm). Is that a big enough difference to make it not start?

 

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