New to CI, so it's probably safe to assume misunderstandings...
My folder structure looks like
.
└── www
├── appthing
│ └── V5
│ ├── application
│ │ ├── config
│ │ ├── controllers
│ │ │ ├── api
│ │ │ └── V1
│ │ │ ├── settings.php
│ │ ├── ...
│ │ └── views
│ └── system
└── vhosts
└── appthing
index.php
.htaccess
My apache config in /etc/apache2/sites-available/000-default.conf looks like:
DocumentRoot /var/www/www/vhosts/appthing
<Directory "/var/www/www/vhosts/appthing">
AllowOverride All
</Directory>
When I navigate to ipaddress/index.php I get an authentication error, which is good, since I can at least access the index.php file. However, if I try to go to index.php/settings I get a CI 404 error. The same code works on my computer (OS X, trying to put it on a AWS Ubuntu 16 instance currently), so it's not a problem with CI semantics.
I think you need to set your Documentroot to /var/www/www/appthing/V5. Normally you should have and index.php file in your CI project which will redirect you to a home (standard = welcome.php) controller.