I was a bit perplexed with this too.. It took me a while to realize I didn’t need to change anything from before I universalized my app. (I’m assuming you’ve already had a normal react app running at this point).

My sites-available config file for nginx used to point to index as first priority. I was confused since I didn’t have a index.html anymore (server.js as you mention), but lo-and-behold it works… somehow… Just be sure to stop your previous pm2 instance, and run pm2 again for your new script

pm2 start build/server.js --name my-project
pm2 show my-project //check to make sure it's all good

Lastly, your port that your app will be running on might be different. For me it changed from 8080 to 3000. You’ll need to update the port inside /etc/nginx/sites-available/myconfig. Here’s what mine looks like in the important bits:

server {
...
    root /var/www/my-project/build;

    index index.html index.htm index.nginx-debian.html // index.html doesn't exist anymore, I really could just delete that

    server_name mydomain.com www.mydomain.com

    location / {
        ...
        proxy_pass http://localhost:3000
    }
}

That’s what I had to do, and I am running React with Razzle as my SSR library (uses webpack and babel)