I can see a few problems that will need to be sorted out. First, look at the 2 back-back Guiding Assistant runs you did starting at 21:09 (RA in red, Dec in green):
The striking difference here is the amount of drift in Dec. The first run was equivalent to a polar alignment error of about 1 arc-min while the second one was equivalent to an alignment error of over 6 arc-min. What happened? I can think of a few explanations keeping in mind that the scope pointing position didn't really change:
1. You have a cable routing problem that is tugging on the guide camera. The pointing position in the first session was Dec=8.8, HA=-1.42 hours and in the second session it was Dec=8.8, HA=-1.15. So you were tracking closer to the central meridian from the west side of the pier, a position that often exposes cabling problems. Keep in mind that through-the-mount cabling, if you're using that, doesn't exempt you from these kinds of problems.
2. Something is loose in the guiding assembly
3. You're using a bad sky model
Of course, trying to use a separate guide scope on a 12.5" CDK is not usually recommended for reasons of differential flexure and trying to do so often requires extreme measures to achieve rigidity in the guide scope assembly. Whether you can get away with it will depend on how long the exposures are on the main camera. You mentioned some kind of "scientific imaging" - are you talking about spectroscopy or photometry?
The next problem is the sudden appearance of spikes in the Dec tracking in your last guiding session:
These are not associated with guiding, they simply "happen", and they appear semi-periodic. Again, these could be coming from a bad sky model or from some mechanical behavior in the payload - things like filter changes, focus adjustments, fan operation, etc. I think it's pretty unlikely they are coming from the basic mount mechanics because the Dec motor would be idle except for sky model corrections and guide pulses.
Overall, I think your mount needs higher-cadence guiding than what you're doing. Since it doesn't have high-resolution encoders, it isn't a good candidate for variable-delay exposures, so I think you should stop trying to use that. Choose a fixed exposure time, perhaps something like 2 seconds, and run with that to see what changes. With your current operation, the guiding is generally "falling behind" the tracking errors, particularly with the large Dec drift.
Hope this helps you sort things out,
Bruce