Hi @SailRN and welcome to the LE community forum 
The problems presented do not appear to be particularly driven by LE nor certbot.
The simplest solution is to switch to an HSP that supports LE (or any other free CA).
[HSP = Hosting Service Provider]
If that is not possible, then you will surely be faced with the never-ending problem of having to manually obtain a cert and then manually adding it to your site [every 60-90 days].
That alone would put me off and have me looking for automation in whatever means possible.
If you have no other recourse, start here:
Getting Started - Let's Encrypt (letsencrypt.org)
And feel free to post any questions you might have or problems you might encounter along the way.