CI in a Linux environment setup

 Hello All,

I am running into so much problems when installing codeigniter in a linux environment and i have no problems when installing it on a windows type environment.
I'll try to explain my problems clearly and what i have tried so far. I hope there is an expert who has installed CI in a linux environment such as CentOS 6 or cPanel that can spot the problem.

Ok so here goes

- So last 3 weeks i downloaded version 3.0.0, i developed my application locally using XAMPP server and i transferred my CI folder to an external server, CentOS 6 root folder (where files are usually called publicly).

- I set up the base_url: http://IP_Address/My_folder/

- As soon as i try to load the application i get a: "Error 404 Page not found"
This message was generated from within the CI error folder: views/error/html/error_404.php so i know i am accessing the file.

What i have tried so far

- Checked php server compatibility
- I looked at countless Stackoverflow solutions such as:
 - Changing the htaccess information
 - Changing the $config['uri_protocol'] = 'REQUEST_URI'; to the other two types QUERY_STRING and PATH_INFO
 - Changing the $config['index_page'] = ""; to $config['index_page'] = "index.php?";
 - lowercase names for the controller filename and uppercase for the class name
- On my godaddy cpanel i used their auto CI installer that installs a fresh CI. This fresh CI worked (showing the initial welcome page).
 - I noticed however, in the config/routes.php, that when i try to change the:
   $route['default_controller'] = 'welcome';
   to
   $route['default_controller'] = 'main/index'; //my controller_name/function_name
   
   I get the same "404 Page error". But when i leave it as 'welcome' and change the views/welcome_message.php data it loads with what i put in it.
   But if i put an <a> link that directs someone to another page (via controller) i get the 404 Error.

I am not sure if it is a route problem happening, setup problem or if linux systems route differently.

Please help . Thank you.