Hello Chris
I don't know all the ins and outs of PHD, most things are on default for me. Polar alignment is the main one for me, and then making sure everything is balanced. Flexure is something you maybe experiencing with your guiding set up but I don't have any experience with it. I have always used a QHY5 in a guidescope and more recently a OAG.
Not much help I am sorry but if you haven't done so already have a look at this regarding drift alignment in PHD2.
http://openphdguiding.org/tutorial-d...ent-with-phd2/
Cheers
Jeremy