If you are having any issues at all with PHD2, slew high and near DEC 0 (for higher latitudes kind of split the difference to stay high) and calibrate each time. It takes almost no time. "Restore calibration" has screwed up way too many people. It works for observatories with fixed everything of course, but it is SOOOO easy to forget to calibrate after changes and end up with mystery problems. It will also clue you into new problems, like inadequate corrections from something slipping.
Run Guiding Assistant not turning off guiding, as then it does an analysis for you of a lot of considerations.
Really, it's best not to over think all this, the PHD2 guys have refined the simpler aspects of this over time. Following their path will usually get you close.
I'm running roughly with guide assistant recommendations now, and guiding at about 0.21" at 540mm on an AP1100, or 0.10 pixels. I love this mount, it just works.