first file shows good primary signal but no secondary, second file is the new coil

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  Matt, in your first file I didn't see that you had captured the amperage for the primary on the suspect coil, probably a good idea to do so.  I see you did in the after replacement capture, good deal.  Also, in that first capture your samples were at 5µs, make sure to keep that down to 1µs when looking at primary/secondary waveforms.  One more thing, I suspect you were using a Beta version of Pico when capturing these waves, be careful to do so at your own risk, many times the program will crash on you out of nowhere, mostly because it is still a Beta.  Also, if people want to view your files, they too will need to have a new beta installed, not the end of the world, just something to keep in mind.
  Now that I have come across as nothing but nit picky, I would like to at least say nice job, didn't mean to be super critical or anything.

hello, thanks for the info on the time base, I'm still playing with all settings. Yes I am using Beta software and i will keep that in mind when uploading. thanks again ;)