The frustrating thing so far is that none of the readings seem to indicate a clear fault of the stator. Typically "sounds like your stator, do the tests" results in "yep, found a short between ..... and ....."
I might add that when you are reading the resistance of the various coils of the stator what you have is a length of copper wire from the plug at CDI or R/R, to the actual coil(s), through the length of the coil of a certain thickness winding, and then back via the other wire. Different types of wires used and joined at the coils because the type of insulation and the stranded wire that are good for the harness are not good for windings and vice versa, otherwise you can just think of the harness and coil as a big loop. If the reading is extremely low it typically means a short in the layers of the windings or even the wires have touched some distance away from the winding. A high reading can mean fraying in the wires causing a poor circuit. An open reading of course means something broke completely. A reading of any value from one coil to another or to the engine case means either insulation on the wires or insulation on the windings has failed and is letting them contact. Winding insulation failure is usually heat related or mechanical damage from bolts backing out of the starter clutch or one of the 3 stator bolts coming out.
If the insulation failure is minimal it may only show up at higher voltages than the meter uses (edit: referring to the internal battery or batteries of the meter which are used as the power source for resistance checks) such as when the charge coils are excited when the engine turns over.
If a charge coil winding is shorted to the stator frame, and the signal coil is shorting or has weak insulation to the charge windings then a voltage induced in the charge coil can make a path of: case-->charge winding-->broken insulation to signal coil-->signal coil lead to CDI--> CDI internal circuitry back to ground at engine. That is what causes the problem, and in this example because of the short to the stator frame unplugging the 3-yellow-wire harness will not "fix" it. If there is a short between the signal coil and charge winding BUT no short to the stator frame then unplugging removes the path to ground via the R/R and that is why it will run.
You can get an idea of the winding just from the specs for it. The trigger coil is a long length of thin winding. This is why it also has a higher peak voltage.
The signal coil is a short length of thicker winding, thus it has a very low resistance. It is basically a 2 foot piece of about 24g wire. Such a short winding generates a fairly small peak voltage.
The charge coils are each wrapped as a single wire that runs on every 3rd post around the stator frame so that when these are all excited by multiple magnet poles in the flywheel the series effect of these windings makes a higher voltage. Thickness of winding is to allow for current flow without overheating. Total of 3 such windings connected in a star mean that when metering actually 2 coils are being measured in series.
I remember one person that had a sporadic problem for a bit, presumably as it was just starting to fail. Heat seemed to affect the problem, although his would start.
One person had the chain wear through the harness where it goes over the front sprocket because the case protector was missing. The problem showed up as cutting out at higher speeds when the chain would contact the wire.
So you need fuel, compression, and spark at the right time.
Fuel --> present and burnable based on header warming
Compression --> not confirmed, BUT: valve clearances checked and ok. engine ran for 20 seconds after starting with electric starter. No 'bad noises' have been mentioned. Attempting to pop start should verify this is not the problem. Was the valve timing confirmed? What type of CamChainTensioner?(manual or auto). When valves clearance was checked no mention of a loose timing chain was made. How hard is bike to pull backwards in gear as this prevents the decompression from activating. Should be almost impossible to pull backwards in 1st (by hand of course)
Spark at right time --> Spark is present. Fuel mixture has ignited and warmed exhaust but won't run. Symptoms match previous examples of spark NOT at right time. Stator appears to pass electrical tests though. NO physical inspection of stator yet though.
Edited by slowriding, 14 May 2012 - 10:18 PM.