I think you have some pretty profound problems with this set-up but there's no evidence that it has anything to do with a meridian flip. Here's the calibration you did at 01:58:
And here's the alert message that PHD2 displayed for you:
01:58:30.559 00.001 1720 Alert: Advisory: Calibration completed but RA/Dec axis angles are questionable and guiding may be impaired
01:58:30.589 00.030 1720 Calibration alert details: Non-orthogonality = 89.931
A 90-degree orthogonality error means the RA and Dec movements, which are supposed to be perpendicular, actually overlaid each other which is what the graph shows. So this calibration was basically useless and any guiding that followed was doomed from the start.. You will need to figure out if this was caused by a cable routing problem or by a mechanical problem with the mount. You can use the star-cross tool as the most basic test of mount performance (Tools menu). Until you can get the mount moving smoothly and consistently at guide-speed in all 4 directions during this test, you won't get anywhere with imaging.
But here are all the other things that you're doing wrong that make it unnecessarily difficult to get good results:
1. You have a sub-par guiding arrangement that results in a very coarse guider image scale of 10 arc-sec/pixel and what is probably a stalk-mounted finder scope that won't be rigid enough for the job. You need to rework this until you can get a guider image scale below 5 arc-sec/pixel, 3 would be better. With your current arrangement, a mechanical shift of the guide camera by only 5 microns (1/10 the thickness of a human hair) you will trigger a guiding error of 10 arc-sec.
2. You aren't using the Calibration Assistant, so you were calibrating in the wrong part of the sky and you were using a calibration step-size that was 2x what it should be. If you intentionally doubled the step-size in an effort to get the mount moving correctly, that was a bad idea and it didn't work.
3. You have changed the default guide algorithms to choices that aren't appropriate for your mount.
Once you fix the obvious problems, you should start over by creating a new PHD2 profile using the new-profile-wizard and doing a baseline performance measurement following the procedure in the attached document. If you continue to have problems, don't start changing all the guiding parameters, that will only make things worse. Your problems at this point have nothing to do with PHD2, they are rooted in various mechanical and operational issues which you can hopefully get sorted out.
Good luck,
Bruce