I was just given a '71 CT1. The previous owner could not get a spark out of the stater.
I got it home and took the stater out only to find both the source coil and the lighting coil were shorted to ground no matter what state the points were in. The coil wires were bent over the stater backing plate. The lighting coil was soldered to the condenser.
The condenser was so covered in solder it too was shorted to ground.
I cleaned up the mess and rewired the parts. The source coil is reading 2.3 Ohms on a Simpson 260 dial meter, 2.6 on a DVM.
I reinstalled the stater back onto the engine and set the points to .013. Using a 1/2 electric drill with the plugs out and the cylinder oiled, spun the engine over at about 60 RPM. ( CCW )
At the pigtails Black wire I'm getting a little over 16 VAC. The service manual I have only list a voltage at 5-8,000 RPM of 200 volts or more.
I know the ignition coil will boost the voltage to 12,000 volts or more at " normal speeds".
The lighting coil is putting out 4 VAC.
The kick started would spin the engine over even less than my drill motor and not checked.
Is the 16 VAC normal at this low RPM?
The condenser is charging / discharging with my meter as the points cycle.
The Yamaha service manual leaves a lot to be desired for the bikes ignition system for troubleshooting.
I plan on restoring the bike for off road riding only.
Still lots to do.

What is your ohm reading with points closed?

The new ignition coil showed up and still no spark. The flywheel and points are clean and new. The condenser checks out charging / discharging with a meter. The readings are almost the same.
16 VAC being generated by the SC and sent to the Ignition Coil with 300 volts being sent to the spark plug.
I'm starting to think the magnets in the flywheel are weak. There are hammer dings in the aluminum flywheel as if the past owners tried to drive the flywheel off of the crankshaft without using the puller. ( I have one )
Weak magnets would produce a weak Source Coil output. You can drive out the magnetism by shocking magnets with a hammer.
The flywheels on my mini-bike engines really fight me as they are placed over the coils due to the strong magnets in the flywheel. I do not feel that with the CT1's flywheel.
I cannot find any data on what the Source Coil puts out with the kick starter? I'm spinning the engine over using a drill motor at about 50-60 RPM.
This has to be faster than the kick starter. I bet the SC voltage is supposed to be a couple hundred volts to be stepped up to 2-3,000 volts as the manual says the Ignition Coil will do.
Now I'm trying to find a company that with re-magnetize the flywheel?

And still no answer to a simple question.

Sounds like you're dead set on following your thoughts on what to expect and how it should work which is okay.   

www.scooterwest.com/flywheel-re-magnetizing-labor-remag.html

Answering markt's question would simply help us move forward in trouble shooting what is wrong.  I have seen flywheel magnets de magnetize, but it was on a questionable brand of chainsaw, and was a known problem.  I don't think the yamaha flywheels were well known for it, but i could be wrong!  Just my 2 cents, hopefully you can get it figured out!  

If memory serves me, you need 30 to 35 ACV to get things to going , haven't experienced Yamaha mag demagnetizing 

Almost all meters are going to give you an "RMS" reading which is an average voltage.  The reading won't even be close to the voltage spike that ignition coil sees when the points open. 

16v AC RMS with points operating properly is likely well over a 100 volt spike.

All of this is why you don't see a "spec".

With points open you should have about 1 to 2 ohms to ground at the black wire going to the ignition coil.  Points closed should have perfect continuity to ground or 0 ohms. Some digital meters struggle...  analog meter with Rx1 scale works well.

I use a digital ohm meter to check the timing, and it comes out very accurate.  I always double check with a timing light.  I have to turn the flywheel very very slowly though, or it will spike voltage and throw the reading off.

I should have said some digital meters struggle.  Readings bounce all over the place and hard to get a clean "points open" indication.

I always use two meters when troubleshooting an ignition system.
A Fluke 87 DVM
A Simpson 260 Analog meter.