On the second file, what are we actually looking at? I'm guessing it represents two revolutions of the engine - or atleast two events where the notch passed the pick up?
Seems that taking a time differential from the beginning of first event to the beginning of the second, correlates to approx 40rpm.
And that individual fluctuations within an event represent over 2500rpm.
40 seems slow, and 2500 is clearly too high. So what is causing the minor fluctuations within each event, surely that should be a clear graph, with a start point as the leading edge of the notch comes by the sensor, a consistant line as the arc passes by, and a drop as the trailing edge leaves the sensor window.
How is the cdi powered, by an exciter coil on the stator plate or battery?
EDIT: the first file once zoomed in looks more informative. That shows the pick up as working.
I can tell you, I once had odd problems with an aprilia rs125. It kept wrecking coils - literally shorting them out internally. After the second replacement coil I began to suspect the cdi. Changed cdi and fitted a new coil and its been fine since.
Have you tested the coil's resistance?