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I communicated that concern to Krydos on Discord last year. I think it happened at a fairly early stage. https://letsencrypt.org/docs/rate-limits/ If you need specific steps to issue an alternative certificate, we may be able to show you the steps. It can be dealt with in Plesk's control panel.

Plesk uses both Nginx and Apache at the same time. Nginx is a reverse proxy sitting in front of Apache and handles all of the static content and html and caching. Apache handles all the heavy lifting in the background. It uses a bit more memory to have both enabled like this but it should give much better performance. We'll see how it scales up to handle hundreds of accounts though.

Yeah, we've had a few problems with .htaccess like this. I'm still looking into why exactly. I've tested FTP, FTPS, and SFTP and they all work for me. One difference that might be messing you up is SFTP is on port 1373 now. On the old Tommy it was port 1342. The reason we changed it was because the SFTP port was a constant cause of confusion for people because all three servers had a different port Tommy=1342, Ricky=1312, and Johnny=1373. So people would search on the forum and find the port of a server that they weren't on and it would obviously not work. To simplify things going forward with adding more and more servers we're just going to keep SFTP on port 1373 for all the servers. Let us know if you find anything else that doesn't seem to be working right.