Why are sub-directories not found - apache

Question

I have been looking at other answers here on stackoverflow and elsewhere, to no avail.
I am running a virtual-host localhost and the homepage of the site is showing up fine, but if I go to any subdirectory/subpage I see this error:
The requested URL /downloads/ was not found on this server
In sum, mydomain.com works, but mydomain.com/downloads/ does not work.
Usually I have fixed this issue with other domains on my localhost by altering .htaccess. Here is my current setup:
Apache2.conf
<Directory />
Options FollowSymLinks
AllowOverride None
Require all denied
</Directory>
<Directory /usr/share>
AllowOverride None
Require all granted
</Directory>
<Directory /var/www/>
Options Indexes FollowSymLinks
AllowOverride None
Require all granted
</Directory>
mydomain.com.lc.conf in sites-available
<VirtualHost *:80>
ServerName mydomain.com.lc
ServerAlias www.mydomain.com.lc
ServerAdmin myemail#mydomain.com
DocumentRoot /var/www/html/mydomain.com.lc/com_mydomain/
SetEnv APPLICATION_ENV local
<Directory /var/www/html/mydomain.com.lc/com_mydomain >
Options Indexes FollowSymLinks MultiViews
AllowOverride all
Require all granted
</Directory>
<Directory /var/www/var/www/html/mydomain.com.lc/com_mydomain/*>
Allow from all
Deny from none
Order deny,allow
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>
000-default.conf
<VirtualHost *:80>
ServerAdmin webmaster#localhost
DocumentRoot /var/www/html
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>
etc/hosts
127.0.0.1 mydomain.com.lc
.htaccess
Options +FollowSymLinks
RewriteEngine On
RewriteBase /
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
I've tried using no .htaccess as well.