I'll add my two cents. Glad to hear you had such good guiding the second time around.
1) I have focus dialed in. But I just made sure my gain for my ZWO Guide Camera was set in PHD2 camera settings not the slider. The slider is more like gamma. There is a setting in the brain part of PHD2 where I set the guide camera to Unity Gain. It took stars from 30db SNR to 70db SNR with no saturation
2) I agree, I have managed to get both pretty close to the same target centerline between OTA and guidescope.
3) I am going back to look at best PHD2 target star calibration position. If I remember correctly, it says that calibration should be done within 20 deg of the celestial equator, but that requires more research on my part.
4) I use Sharpcap to get PA. I like the fact that Sharpcap gives a right/left/up.down metric.
5) I marked the RA axis with reflective tape pointers to define my physical home position (just a little off of weight down position). It made my EXOS2 perfect for GOTO’s. Target is always in camera frame first time.
Scope: Orion EON 115mm APO
Mounts: ES EXOS2-GT w/ PMC-8
Cameras: ZWO ASI 071MC Pro, Canon 6D Mk 2, Canon 7D2, EOS 60D Asto Modified
Lens: Canon EF 100-400mm f/4.5-5.6L IS II
Misc: TELRAD, ZWO ASI120MM Guide Camera, Astromania 60mm Guidescope, Senso Sesto Focus Motor
Software: EXPLORESTARS IOS & WIN, Stellarium. NINA, APT, DSS, PixInsight, Photoshop CC
Computer: Dell Latitude E5450, Windows 10