Question #1: You can use any valid certificate from the server on which you've installed Jot Server. Usually we are using the same certificate which is installed for the domain, because you should add domain url as server's url to the Messenger settings.
Question #2: Yes, in your case you should edit config/config.json file manually every 90 days. Also I think it is not so hard to create small script which allows to update config.json file with new params every 90 days automatically. If you use forever plugin or something like that to run Jot Server, then Jot Server will be restarted automatically when any of the files defined as watchDirectory is changed.