It kind of looks to me like you threw everything together and started trying to image, expecting everything was going to work just fine. As you found out, it didn't. I think you need to back up and invest time in testing your new setup and getting it working correctly before trying to do automated imaging. It looks like you spent the first 45 minutes trying to use a calibration done two nights ago, but a later calibration showed that the guiding assembly wasn't in the same orientation. So the first 45 minutes can't tell us anything. When you finally did a new calibration, the Calibration Assistant told you it was a poor result - which it was. Plowing ahead with a bad calibration will generally just produce bad results. With the strain-wave mount, it's possible that you don't have the luxury of using 3-sec guide camera exposures. A large periodic error in the mount will often create orthogonality errors in the calibration. I can't see that you ever did a Guiding Assistant run, but the limited guiding data we have suggest your polar alignment error was very large, perhaps 25 arc-min. And of course, all of this was further muddled by all the lost-star events. The fact that you didn't take the time to build a dark library was a further complication. I think it's possible your OAG/Guide camera assembly may have some problems, for example guide camera focus, looseness, or positioning of the pick-off prism. Obviously, until you can eliminate all the lost-star problems, you're not going to get much insight into the guiding performance. That's the place to start - you probably need to reliably get usable guide stars with 1-second exposures at this point. After you've gotten there, get a baseline set of measurements using the attached guide. I would extend the testing to include 20-30 minute guiding sessions on each side of the pier.
Good luck,
Bruce