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As Forchetto said, the regulator has nothing to do with ignition. It has to do with keeping the battery charged and nothing else.
Batteries on non-running quads measure 12.6 volts (or lower if it's partially discharged). So how did you get 13.5 volts? I would measure that again. Maybe you had a charger hooked up at the time?
Regulators are easy to test. You start up the quad, rev it a little, and measure the battery voltage. The charging system (which includes the regulator) should raise the battery voltage from 12.6 volts to somewhere between 13.5 and 14.5 volts DC. So forget about testing the regulator until the quad is running.
42 VAC for the ignition power winding sounds low to me, but I can't imagine a fault in the stator that would cause the output to read a little low. Usually it is OK or measures really really wrong. I think you would still get a spark with 42 volts AC. The output voltage of the stator varies with cranking speed (as Forchetto said).
Next I would measure the voltage on the kill switch pin of the CDI while hooked up and while cranking. This is a complicated waveform, so take both DC voltage and AC voltage measurements and report back.
You really do need to measure the trigger winding voltage. Just because it puts out a small voltage doesn't mean it isn't as important.
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