I haven't gone back through and read this whole thread but I assume you have this part of the config.json down solid?
/* If you have https server (recommended) you need to fill 3 fields below */
It took me many, many attempts to get that exactly right.
Also your app.js is running and as a daemon? I ended up using forever so my statement is:
forever -w --watchDirectory=/etc/letsencrypt/live/mydomain.name start app.js
sudo forever list ## to verify its running
Let me know what you find