Hi Ventura, thanks for doing a thorough job of collecting useful data. The biggest problem you have at the moment is a huge periodic error in the RA drive:
This shows a periodic error of about 40 arc-sec peak-peak which is pretty bad. Periodic error is typically a problem with these strain-wave mounts but I would say this is unusually large. This is coming from a mechanical tracking error that occurs at a period of about 440 seconds:

This problem is why you generally can't get the RA guiding RMS below 1 arc-sec and it's also why you're having so many problems with the calibrations. I think you should take this up with the manufacturer and see if you can get it repaired. In any case, you probably won't be able to use guide camera exposures greater than 1 second because the mount requires essentially constant corrections. If you are going to be stuck with this for some period of time, you could try guiding in RA using the PPEC algorithm, giving it a period length of 440 seconds and disabling the 'auto-adjust' checkbox. If you can get suitable guide stars using 0.5 sec exposures, you can also do that. All of this will help PHD2 to mitigate the mechanical problem.
On a different point, it looks like you have a pretty sizable polar alignment error, reflected on both sides of the pier. Here's the Guiding Assistant view of that (Dec is in green):
This is about an 8-10 arc-min alignment error, which is not a big deal but you could probably improve on it without much effort. It will also mean you will have fewer Dec guide corrections that need to be made which will help maintain a rapid guiding cadence.
Hope you can get some assistance on the RA drive problem.
Bruce