With the "PICO" you should be able to test the entire circuit on a cylinder including DME and sparkplug spark. For function, shorts, resistance, what ever.
With a two channel you could compare Cylinder 1 to another cylinder or CPS signal.
Or the cam signal. Or any other electrical signal.
The "PICO" website has tutorials on running tests on various systems.
It has a good tutorial on Coil on ignition systems including the three wire coil.
It explains function of each of the three wires.
I read the info and from it I learned that the area you have circled in blue in post #126 is (VS 42) is a constant Voltage Supply point.
The tutorial also includes known good waveforms and how to read them.
You could also go to youtube and look for "Scanner Danner" he has many videos on using an Oscilloscope.
PICO is a great diagnostic tool I wish I had one.
But the caveat is: If one doesn't know how to use it then it is of no value
After attempting to help with your issue and following everything you have tried.
It looks like most of the problem is with cylinder 1.
Although I know zero about waveforms or "PICO" it does seem that the issue with cylinder 1 is electrical.