Hi Howard
The final steps in Terry's advice are to do with storing the PEC curve in the mount itself and let the mount apply the corrections - permanent PEC.
If you are going to be using EQMOD anyway (the only alternative is Skywatcher's ASCOM drivers, or ST4), I would begin with using EQMOD to apply the PEC and then consider permanent PEC later after you have everything sorted to your satisfaction. Personally I don't see that permanent PEC has any advantages over EQMOD applying PEC but opinion is divided on that point.
Re setting up AutoPEC, I would train it over the full 9 cycles rather the minimum of 5. This should give a cleaner and more accurate PEC curve. I looked at your logfile using PHDLogViewer and checked its frequency analysis of the long 3h 47m guiding session. It shows a single clean peak at around 480 seconds which is the worm period for the EQ6R and should be very easy for PHD2 to guide out, and later for PEC to correct.
However before you embark on PEC I think you need to take a good look at your guiding. Your RA guiding is an endless sawtooth of corrections. I note you are using Predictive PEC as the RA guide algo and I am not familiar with that algo and its configuration but a sawtooth pattern like this usually indicates that guide corrections are too aggressive.
I have the EQ6R too, and the similar AZ-EQ6, and I use the default hysteresis RA guide algorithm with low settings for aggression. I have experimented with PEC but found that it made little or no improvement to my overall guiding. I do find that these mounts generally work better with short, 1s, exposures and I only increase the exposure time if that is the only way to improve the SNR of the guide star. For me the biggest factor is seeing and my RMS can be anywhere between 0.6 and 1".
My recommendation would be that you change from the PPEC algo to Hysteresis and experiment with its settings (i.e. aggression and MinMo) to achieve the best guiding and only then try PEC, or revert to Predictive PEC but this time with a better idea of what your mount is capable of.
cheers
John