Hi John. There's no way for anyone to automatically set the dithering and settling parameters for you, they always depend on the mount. So you will need to do some homework and figure out what makes sense for your rig. You can start by looking at the guide logs and seeing how the mount behaves after a dither is done. Here are a couple of examples where things didn't settle within the time period you specified (RA in red):
The Y-axis is shown in units of pixels because we're talking about dithering. The settling requirements you're using require that guiding error will be less than 1.5 pixels for a period of 10 seconds with an eventual timeout after 40 seconds. Your choices are probably these:
1. Relax the settling constraints
2. Reduce the size of the dithers
3. Don't continue working with a bad calibration - the one you're using triggered an alert, probably because you didn't manually clear the Dec backlash before starting the calibration
4. Improve the guiding performance
On the fourth point, the RA tracking seems to have a lot of abrupt excursions that interfere with settling. You should be binning the guide camera, for sure, and then perhaps finding ways to tame the native tracking error in the mount. When you bin the camera, use the new-profile-wizard to create a new profile for the binned operations. All of the dithering and settling stuff resides in your image automation app, PHD2 is simply doing as it's told including reporting timeout errors.
Good luck,
Bruce