So I am hitting problem number 3 today.
I avoided the upgrade issue by simply not upgrading (after trying 3 times, I got tired or reflashing the SD card). I am waiting for a second GPS Dongle as the GPS problem might very well be a hardware issue.
Now, I finally launched my profile. I started with just the mount (NexStar to which a 6SE is attached): connection was successful, and it properly tracked the moon for 10 minutes. Then I added the ZWI driver for the ASI224 that I plugged instead of the eyepiece, and from that moment on, the NexStar stopped connecting. I restarted the RPi several times, restarted the controller, re-created the profile from scratch. The problem is always the same (see image). I am a bit at a loss.