You say ohm tested the rectifier.
There are six diodes in a four wire rectifier Did you individually test all six with the meter polarity one way and then the reversed way. 12 readings altogether. Each diode should have given infinite resistance one way and a very low resistance the other.
It is actually better to use the diode test range of a multimeter than one of the ohms ranges.
Are you checking the voltage between the red DC output wire from the rectifier and ground. Did you rev the engine when testing the volts
ohm testing the stator coils will not tell you if a small number of turns are shorted.
CDI electronics' trouble shooting guide gives more detail.
http://issuu.com/cdielectronics/docs/practical_ouboard_ignition_troubles