If you want to use Let’s Encrypt, why not use the Let’s Encrypt tools we provide at https://app.infinityfree.net/ssls ? Those are designed for our hosting and are extensively tested so we know they work.
Let’s Encrypt’s HTTP validation doesn’t work. The reason is described here:
Using Cloudflare works, but using Cloudflare to get a Let’s Encrypt certificate seems like an unnecessarily cumbersome workaround. If you’re going to use Cloudflare, why not use Cloudflare’s SSL?