Now is time for an update. I finally figured out what was preventing sparks, and now have ignition again.
I checked again the voltage at the CDI box, and even without cranking, it was only 6.5-7V.
The voltage at the front fuses was a solid 13V, and the voltage at the engine fuses was only 6.5-7V.
I checked my ground connection but that was fine.
I opened the 14 pin connector, and sure enough there was a connection holding by a thread that broke immediately. I resoldered it and voila, my ignition is back.
