Sorry but I'm sick as a dog and have to log out for the night. I'll be back on in the morning to assist you.
I could only find the 1998 test specs, but I think they are the same as your sled. You have a pick-up or triggering coil, a charge coil and lighting coil under the flywheel, A CDI box and ignition coils in the system. By unplugging the black wire you have bypassed the safety switch and kill switch, so we know those are good. Your lights light up when you pull it over so the lighting coil should be good.
Use the test specs on the diagram to test the other stator parts. Your pick-up coil should produce a tiny pulse of .5-2 volts AC when you pull it over. That is on the blue and red wires and that test is not in the manual. Don't forget to test the stator plate ground wire (brown) to ground. You should have reading showing it's grounded to the engine block.
You are looking for an open or closed circuit that would indicated a broken or shorted wire. Ohm tests of the CDI box are inconclusive so you want to eliminate as many items as you can. Even the factory testers are hit/miss on the CDI boxes. The most common failure is the pick-up coil. (Also called a triggering coil, timing sensor, etc. It reads the little timing tab on the flywheel and tells the CDI when to fire.)
If this does not match your wiring, let me know and I'll try and find the 99 model in the morning. From what I remember, the ignition was the same.