1. I use the SKYX or PEMPRO for polar alignment on my CEM120EC2 as I cannot see the pole. I really like PEMPRO. While it costs some money, you don't ever need to see Polaris and the wizard is easy to use. You can also use it to create a PEC curve if you have a mount without encoders. I bought my copy 5 years ago and it still works.
2. I have never had a runaway slew. I would wonder about the software you are using more than anything else. Remember, just one click of the mouse when you are pointing to something on the screen can, if you don't have "confirm slews" turned on send the mount off on a slew.
3. I keep the hand controller disconnected for much the same reason. It's just something that can short out and cause problems.
4. Everynight a do a find zero. My mount is parked pointing at Polaris. It moves a little. I then do a trial slew. If the object is in my FOV then I'm good for the night. If it's not then I do a pointing model which takes about 15 minutes to do 20 points.
5. I don't use the GPS. My computer keeps the time accurately enought that it's never been an issue. I have an internet connection and I just update the time on the PC and then push the PC time to the mount.
6. Unfortunately I don't use either PHD or Stellarium - I use MaximDL or the SKYX to image. I have always been afraid of bugs in freeware products and I know that no one tests them in an integrated manner with each mount that comes out.
7. Make sure that you have the latest motor and mainboard software up and running. The early versions did have bugs but the one's from June of 2018 onward have been robust for me.