Hi Tom, I will try to answer some of your questions:
1) PPEC and guiding is fighting each other. The fact is when you enable PPEC, the corrections are managed by mounts electronic and Ekos/INDI don't know, which corrections is the mount doing. So if you also turn on guiding, and Ekos is sending the corrections to the mount, they fight each other. It is possible to enable PPEC wth guiding, but this PPEC will not be the one which is ctored in the mount. For this purpose ther is a GPG RA algorithm in Ekos, or altenatively VS-PEC in ASCOM (EQmod driver). The reason why your PPEC was turned on and of was that the guiding pulses  from Ekos tried to compensate while PPEC was runing.
2) There is no PPEC  file stored in Ekos so far. The best way, how to create nice PPEC curve is to record it under ASCOM with PHD2 and EQmod. Then, as you mentioned, you will need to average and smooth the curve in the PECPrep and record it again using PHD2 and EQmod under ASCOM. After this, you will be able to enable it under INDI/Ekos, but don!t try to enable aslo guiding (as I mentioned in previous text).
I hope that I have answered your questions.

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