I would almost bet on the CDI, seems like every time i get one with a no spark condition the first thing i do is just grab a spare CDI and toss it on and it fires up. I go through CDI units like arse wipe here. I replaced six of them this summer alone on a junkers i got running and fixed up for people.
If you have a voltmeter set it to AC volts, put the positive lead on the black/red wire and the negative lead to the motor case, pull it over a few times, you should see voltage. If it was an electric start you can usually read around 10-20v AC output on that wire when spinning it over with the starter. But even with the recoil you will see voltage, if you have an analog voltmeter that works even better for this cause you can see the needle swing on the meter faster then you can see the digital meters digits change up and down.
I made a test light for checking them this year, my old faithful one broke. I just took a 24v bulb, but a 12v bulb would work to its just what i had laying in the junk box, and put a clip lead on for the ground and a bullet connector to plug into that wire. Its definitely possible you have a problem with the stator coil if water got in there and corroded it all, but usually even then i find its just a broken solder joint and a quick touch up with the soldering iron gets it working again. Its just a coil of wire, unless it gets really messed up there isn't much to go wrong.
Check your kill switches, and even disconnect the wire to them, usually the black wire from the CDI unit, can't count how many times i fought a no-spark condition only to find out it was a rusted up kill switch shorting the kill wire.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....