Hmm... Seems like a meter issue then too. I can't see you having two ignition coils with no resistance on the secondary at once, especially when one is new. I mean i guess its possible its bad, but still odd.
You should have way more volts from the CDI to the coil, around 100+ volts AC output from the CDI. I would have to measure mine again but i think on my 200ES the ignition coil wire was around 90v at idle and 100+ at higher speeds.
For now my guess is this... You have a bad stator/source coil if, and i say IF, you know for sure that the CDI is good. Because even if the ignition coil is bad you should be seeing far more voltage out of the CDI. Thats why i said if you know for sure the CDI is good then the voltage source, aka the stator/source coil, has problems. Also the fact that you weren't seeing 100-400 ohms on it.
But, before you toss a crapload of cash at it.... Borrow or buy another meter just to double check! Because it seems your getting some odd readings.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....