Permalinks are not working in wordpress.

I have looked at all the similar questions, and I am still not able to get permalinks to work. I have confirmed that .htaccess is being accessed. I have also confirmed that mod_rewrite is enabled, and working, and even working in .htaccess. I will explain how I have tested this.

When things first weren’t working, I removed the rewrite rule in my /etc/apache2/sites-available/mysite.com.conf and confirmed that I was able to get the site to load without https. I then inserted a bad line at the top of my .htaccess file, and it gave me a 500 error. I then removed that line, and added the rewrite rules that were originally in my mysite.com.conf file to the .htaccess file, and I inserted it between <IfModule mod_rewrite.c></IfModule> tags and tested it. I was redirected to the secure site. I am able to go to the page if I leave the default permalinks alone, but when I change them to anything besides “plain”, I get a 404 error.

Here is my .htaccess file as it sits now. The wordpress rules don’t work, but the HTTPS rules do.

# BEGIN WordPress
<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /
    RewriteRule ^index\.php$ - [L]
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule . /index.php [L]
</IfModule>

# END WordPress

# HTTPS Rewrite
<IfModule mod_rewrite.c>
    RewriteEngine on
    RewriteCond %{SERVER_NAME} =mysite.com [OR]
    RewriteCond %{SERVER_NAME} =www.mysite.com
    RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
</IfModule>

# END HTTPS Rewrite

Here is my current mysite.com.conf file:

<VirtualHost *:80>
    ServerAdmin webmaster@mysite.com
    DocumentRoot /var/www/mysite.com/html
    ServerName mysite.com
    ServerAlias www.mysite.com
    ErrorLog /var/www/mysite.com/logs/error.log
    CustomLog /var/www/mysite.com/logs/access.log combined
    <Directory /var/www/mysite.com/html/>
        AllowOverride All
    </Directory>
</VirtualHost>

sudo a2enmod rewrite tells me “Module rewrite already enabled”

For additional information, I followed How To Install WordPress with LAMP on Ubuntu 18.04. I also followed all the prerequisites, including initial server setup, install a lamp stack, and letsencrypt guide for apache. I even rebuilt the server and started from scratch when it wasn’t working.

Needless to say, I am a bit perplexed. Any help would be appreciated.