Oh, wait.
Something is fundamentally broken. Something is broken in your configuration, you don’t need a guide to Let’s Encrypt, you need to figure out what broke. You shouldn’t need to do anything to make those files exist. When you request them in Virtualmin, they get created (and also deleted immediately after validation).
So…I have no idea what’s going on.
Are you seeing these log entries in the right virtual server log? It’s possible you have a “wrong site shows up” problem, caused by having some VirtualHosts configured with *, while others are configured with IPs. (See Website Troubleshooting – Virtualmin). Other causes of “wrong site shows up” includes IPv6 misconfiguration.