Well that was painstaking but think all my domains are setup with the acme.sh setup now and from this point on they should auto renew once I add the cron job. I will run it manually in like a month or two just to make sure it works though.
The basic domains that just have a simple www sub and that's it are easy. It's the ones that have other sub domains then I need to alias the validation folder to the root, and for some reason it was not always working correctly. Often times I had to make changes, change it back, then change it back again and suddenly it would work. It's really messed up. It's like changes would not take unless I changed the config file, restarted the server, then changed it back, then restarted again.
So glad this is over for now...
I do eventually want to code myself a web interface to fully manage servers though, like everything from setting up new domains, users, email mailboxes and everything in between. I've only been telling myself this for like 10 years... lol. Just need to take the time to actually code it and once it's done it will make my life easier. I can just keep building modules any time I want to automate something. My goal is to set it up so I never have to manually edit config files ever. Basically something like cpanel but without the price tag.