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Try removing the following line:
RewriteCond %{THE_REQUEST} ^.*/index\.php
Since the line below it matches URIs that end with /index.php only, you don’t need to add a condition for it. Also, don’t forget to escape the .php dot in ^(.*)index.php$.
RewriteCond %{SERVER_NAME} =www.<ommitted>.co [OR]
RewriteCond %{SERVER_NAME} =<ommitted>.co
RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
What are these lines for? Are you redirecting all traffic from HTTP to HTTPS? The VirtualHost you posted is configured to listen on port 80 only—make sure you’re adding the rewrite rules to the right VirtualHost.