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 */
root: '/folder/with/https/cert/files',
cert: 'myfilename.cert',
        key: 'myfilename.cert',

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