From a quick glance at that tutorial you should be running this default.conf.
The relevant lines for serving static files are these ones:
root /var/www/;
and
location / {
# This is cool because no php is touched for static content
try_files $uri $uri/ /index.php?q=$uri&$args;
}
This means that Nginx returns a file if it is found OR loads index.php, passing it the URI and args. The root directive means that it only looks for files under /var/www. So if you have a folder at /var/www/js with a file inside it called my.js you should be able to load it by visiting http://<your-domain>/js/my.js.
Where are you trying to serve these js files from. What's the exact full path to them? Comment below and I'll keep editing this answer till we can figure it out.