Updated on January 3rd, 2020.
Some potential solutions to my 2 earliest problems.
Problem A
As we are running under a native installation in AWS, Here is what I did.
In /etc/ssh/sshd_config, I replaced
AllowUsers automated_user #automated_users_allowed_to_ssh
by
AllowUsers ubuntu automated_user #automated_users_allowed_to_ssh
And then, I ran
sudo service sshd restart
I was then able to remotely login through ssh again with user ubuntu.
Problem B
I might have a follow-up questions with regards to /edx/etc/lms.yml and /edx/app/edxapp/lms.env.json, but for now I was able to add the correct values in /edx/etc/lms.yml.
I first had to run the following commands:
sudo -H -u edxapp bash
cd ~
source edxapp_env
source venvs/edxapp/bin/activate
cd edx-platform
python manage.py lms generate_jwt_signing_key
The last command generates values for JWT_PUBLIC_SIGNING_JWK_SET, JWT_PRIVATE_SIGNING_JWK and JWT_SIGNING_ALGORITHM that needs to be filled in into /edx/etc/lms.yml.
And after restarting the LMS and the CMS, I was able to login again with my regular user in the LMS and the CMS.
I don’t know, if this is the “official” solution but it did work for me.