Keep in mind that the single winding has very fine wire so there are many turns of wire on the post. This is done to maximize voltage, but does not deliver much current. A meter that draws too much current may not show a high voltage. Voltmeters can also "average out" the AC reading and show less than you expect. Think of an AC sinewave; the peak voltage only exists for a short duration at the very top of the wave. This is where an oscilloscope can be handy since it can register fast enough to show the actual waveform.
Since you're getting 5-6 volts, assume it's OK and move on to the CDI. Most of the time electrical problems come from bad connections. Inspect all the pins with a strong magnifying lens.
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2011 EC250E
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