Hey Jeremy, to make sure we don't get confused, The only thing you need to configure on your UNA Website for messenger to work is the URL and Port number like you pasted above. Now, from here on, I will be talking about the "other server" that you are running Jot Server on.
You stated that you have another server that you are running Jot Server on correct? So on that server, login to your application that is used to manage your server (i.e. Plesk, cPanel, etc.)
In the server settings, go to the "Firewall" settings. If the port was opened properly, you should see an entry with something like this assuming port 5443 is what's used:
Jot Server Allow incoming from all on port 5443/tcp
If it is there, then you are good. If not, you will need to add it.
Now, go into the config.json file that is on that server and make sure you have it configured correctly similar to this
You will need to update the "root" to reflect where your actual certificates are stored, and the correct cert/key names. More detailed info about this HERE
Note: Make sure that the cert you are using is valid and not expired.
Once you have confirmed all of this, you can try going into the directory where Jot Server is installed and do a forever stop app.js,then wait a few minutes and do a forever start app.js
You can then go back to your UNA website and make sure you have the messenger settings setup with the right URL and Port that is opened on the "other server" for Jot.