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I've been manufacturing CDI units for about 13 years, and I think that when trying to diagnose a problem or test an ignition unit, it's important to know what type it is.
A CDI system doesn't have 12v applied to the coil, but rather discharges a capacitor that's been charged to several hundred volts into the coil primary in an extremely short time when it's time to fire. You can't just connect a voltmeter to the coil to test anything with this type, for example.
The transistor switched ignition system that our Ninja 250s use does have 12v applied to the coil, and the ignition unit grounds or ungrounds the negative side as needed. Checking that 12v is applied to the coil is a good test with this type of system, to see if the wiring and switches are working correctly, and other tests can be performed with simple procedures.
Since you mentioned that you suspected an ignition problem, I thought it might help to let you know that you're not dealing with a CDI system here. But from your reaction, maybe you would be better off somewhere else.
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