I got it to work by making a universal vhost alias for ./well-known like this
Code:
Alias /.well-known /var/www/LEwebroot/.well-known
<Directory /var/www/LEwebroot/.well-known>
Options FollowSymlinks
AllowOverride All
Order allow,deny
Require all granted
</Directory>
while having calibre-server running like so in apache
Code:
<VirtualHost *:80>
ServerName my.vhost.com
RewriteEngine on
### For letsencrypt ###
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^/(.*) http://another.path.to.the.alias.com/$1 [P]
### Letsencrypt fin ###
RewriteRule ^(.*) http://localhost:8080/$1 [proxy]
RewriteRule ^ http://localhost:8080 [proxy]
SetEnv force-proxy-request-1.0 1
SetEnv proxy-nokeepalive 1
</VirtualHost>
I hit my rate limit testing so I cannot verify this, but the script made it past the url auth step, huzzah.
EDIT: Nevermind. That breaks the server