This is going to be a long response. We can start with some operational problems and mis-conceptions you have:
1. Your guide camera is running in 16-bit mode but you've specified a saturation-adu of 255, which is only appropriate for 8-bit cameras. This degrades the auto-find procedure and forces PHD2 to use sub-par guide stars. Change the saturation-adu value to something appropriate near 65500.
2. The Calibration Assistant will always do a better job than you can. When you slew manually, you're probably not clearing the Dec backlash/stiction sufficiently in your mount which leads to problems such as orthogonality error. In one of your calibrations, you got a lot of lost-star events so obviously that calibration was useless. If you have some reason to want the calibration slew to go elsewhere, just change the 'target' values in the CA window - that's why they are there. You can even save and re-use them as a "custom" location. The important thing is to stay close to Dec=0 and not pointing down close to the eastern or western horizon.
3. Your worry about large Dec corrections is unwarranted. Those are Dec backlash compensation pulses and yes, they are needed for your mount because of its mechanical behavior. You should focus on the results of the guiding, especially the RMS values of both RA and Dec rather than guide pulse sizes.
4. Your fiddling around with guide settings has been generally futile and in the case of PPEC, counter-productive. The problems you're having at the moment are coming from the mount and you will not be able to mask them with guiding.
5. The last guide log you sent was done with shift-lock enabled in NINA, presumably because you were trying to track a comet. This makes it nearly impossible to analyze your guiding and/or mount behavior.
Now to the mount-related mechanical issues:
There is a lot of periodic error in RA, I would say considerably more than what is expected with an iOptron mount:
This is the unguided tracking behavior of the mount showing a peak-peak periodic error of nearly 30 arc-sec.
It is mostly attributable to a periodic error that roughly matches the worm period on the mount:
This large RA periodic error creates RA drift during calibration which is probably the main source of your orthogonality errors. Although PHD2 is doing a reasonable job of trying to cope with this, it was hampered by your fiddling with the guiding parameters. This, coupled with using 2-sec exposures, leads to pretty consistent under-correction in RA - PHD2 was generally falling behind the tracking errors:

I think you should discuss the uncorrected PE with iOptron - I think they will agree it is too large and will help you improve it. They are certainly familiar by now with the kinds of graphs I'm showing you. In the meantime, you can try to help PHD2 manage it a bit better by using 1-sec exposures and using PPEC parameters of 0.9 for predictive gain and 0.7 for control gain. Set the period length to 348 and disable auto-adjust. Again, this is just a temporary measure, you should find a way to improve the mount mechanics. We have seen many cases where iOptron mounts were simply meshed too tightly and could be improved rather easily. I suspect this is also what's behind the occasional large RA excursions you are seeing. Beyond that, I strongly discourage you from doing any other fiddling around with guiding parameters.
If you really want to get a clear view of the mount's limitations, you can follow the procedures in the attached document. Note that the procedure must be done with no imaging and no involvement from your imaging application. I would probably extend the recommendations in the document to suggest getting 20-min guiding sessions on both sides of the meridian.
Regards,
Bruce