You may well have multiple problems here. For sure, you have a problem with the mount payload, something that is allowing the guiding assembly to move around. You happened to produce a clear example of that with the GA run, something that doesn't often happen. Here's the GA run results, RA in red, Dec in green:
Look at the giant Dec excursion about midway through the sequence - an abrupt 7.5 arc-sec excursion. At this point, the Dec motor was not running and no guiding was being done. This seems like a pretty clear proof that something is moving around on its own.
We see other excursions like this on both sides of the pier although not as dramatically, so I don't think it's safe to assume that everything is fine after a meridian flip. Here's an example when the scope was pointing about 7 degrees west of the meridian:
This affected both axes as you can see. Because of the coarse image scale and the tiny guide camera pixels, the 20+ arc-sec excursion is equivalent to about 15 microns of shift at the camera sensor - something like 1/3 the thickness of a human hair. These things can be fiendishly hard to track down.
All of that said, it's quite possible that these large, quickly corrected excursions aren't really the source of the elongated stars. Instead, you may be dealing with differential flexure between the guide scope and the main imaging scope. In order to know that, you need to look at individual frames that have elongated stars, determine the start and stop times of those exposures, then look at the PHD2 guiding log for those exact time periods. If you find even one such image that doesn't align with a guiding segment with large excursions, you should start looking at differential flexure. My hunch is that you probably have that problem as well.
Good luck,
Bruce