Ok, between the PM's we've been exchanging and what I've read on here, I tend to agree with the CDI being the problem.
Here's what we know: Even though the ignition coil under the seat tested out of spec, those readings don't matter if you're not getting 12 volts to the coil to begin with. Since the stator plate coils behind the flywheel tested good, they can be ruled out. I assume you've double- and triple- checked all the electrical connections between the stator plate and flywheel and found them to be good.
Since all the TORS equipment has been uhooked (brain box, throttle switch, and carb. cap switch), that can be ruled out as a cause of your problem.
You're NOT going to get enough volts from the source coil behind the flywheel when just kicking the engine over to light up the test light. The engine isn't spinning over fast enough. The CDI box, when working properly, steps up the voltage going into the igntion coil to 12 volts.
Assuming you still can't get 12 volts TO the ignition coil with the kill switches unhooked, it sounds like the CDI box is indeed bad. You did check the ground wire that bolts to the back of the ignition coil, correct? Its nice and clean and tight?
I don't think its worth the extra $$ for a Hotshot CDI box. Somebody (awk, I think?) has had trouble with them. Just get a good OEM replacement and run that one.