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Yes, your PHD graph is awful ! I've been "getting to know" my second hand NEQ6 over the last few months too, I feel the pain !
I reckon your polar alignment is fine, the 0.43'' RMS is typical for seeing.
RA guiding looks like the mount is not getting enough corrections, or not responding to the guide commands properly. I see about +-15'' drift in RA when not guiding, so the guiding commands do seem to be getting through eventually, since you're getting about +-3''.
In fact, on your graph there's a couple of minute periods where RA guiding is OK (probably correspond to periods when the unguided plot reaches plateaux on the the main +-15'' sine wave).
Don't suppose you have a small Max RA duration in the PHD settings limiting the corrections being sent ? If you haven't already tried, you could also set the mount auto-guide speed up to 1X, and up the aggressiveness.
I've found that 1s intervals give me best results in PHD with an ED80 and RC8 (ST4 guiding and guidescope). I don't think moving up to 5s will help control RA guiding.
You could also try guiding at say -70 to -80 declination to see if your setup can keep up with guiding there (ie when much shorter RA guide commands are needed).
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