I'm happy to help. Astrophotography is indeed a journey and the learning curve is always present.
Dark optimization usually "just works" but sometimes it doesn't as you're finding. The best solution is to use exposure and temperature matched darks so you don't even need it. Looking at the fits headers it seems that you have this. If you're seen a noise difference between when it is used and not used it may need adjustment. In this case you'll need to try adjusting the settings in ImageCalibration re: dark optimization. I've not done this before - perhaps someone else has something to add on this point.
Before you mess with those settings you can try calibrating the flats w/ just the bias or use darks specific to the flats to match temp/exposure. If the flats are short enough using a master bias to calibrate them may be all you need. It depends on the camera. I'd say give it a try and see what you get.
You might also try using the CosmeticCorrection tool with a master dark as a reference. This will help clean up lots of things in the lights like hot/cold pixels and bad columns/rows. I do see some dark columns in your lights so it may be worth investigating this as a part of your process.
I've had raised donuts myself. Unfortunately not the tasty kind.
In most cases this is caused by a shift in the projection of the dust on the sensor, whether by just movement of the dust, inaccuracies in the filter wheel, rotator, difference in focus, etc. The CloneStamp tool may come in handy here. Some people use clever formulae in PixelMath.
Share the final when you're happy with it!
- Greg
