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Any ideas on how I could easily confirm / eliminate the RA axis from the list of potential causes?
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You could try close to 90 deg declination in Octans, and even turn off tracking on the mount. This should show how much PHD wobble there is for stars which really are stationary in the sky.
You would also need to enter calibration data in PHD (if you haven't already calibrated somewhere else), and set it not to send guide corrections to the mount. This way you would just use PHD to plot the unguided movement of a guide star for you.