Integrating a codeigniter site as a wordpress plugin

I have a partially completed plug in from another developer for WP that integrates the Codeigniter based Easy!Appointments scheduling utility into the WP database. I need to associate the Easy!Appointments user with the WP user.

STRUCTURE: The Easy!Appointments database is part of the WP database structure in mysql. Easy!Appointments is built in the Codeigniter Framework. The plugin will let Easy!Appointments run on a page with a short code but WP headers are missing. So, I am running it in an iframe within a WP page. The main part of the plug in is:

    <?php 
/**
 * Plugin Name: Easy!Appointments - WordPress Plugin
 * Plugin URI: http://easyappointments.org
 * Description: Creates a bridge between Easy!Appointments and WordPress.
 * Version: 1.0.0
 * Author: A.Tselegidis
 * Author URI: http://alextselegidis.com
 * Text Domain: eawp
 * License: GPLv3
 */

/** Base Plugin Path */
define('EAWP_BASEPATH', __DIR__); 

/** Supported Versions */
define('EAWP_MIN_VERSION', '1.0');
define('EAWP_MAX_VERSION', '1.0');

/** Setup Autoloader */
require EAWP_BASEPATH . '/core/Autoload.php'; 
$loader = new EAWPCoreAutoload; 
$loader->register();
$loader->addNamespace('EAWPCore', EAWP_BASEPATH . '/core');
$loader->addNamespace('EAWPCoreInterfaces', EAWP_BASEPATH . '/core/interfaces');
$loader->addNamespace('EAWPCoreExceptions', EAWP_BASEPATH . '/core/exceptions');
$loader->addNamespace('EAWPCoreValueObjects', EAWP_BASEPATH . '/core/value-objects');
$loader->addNamespace('EAWPLibraries', EAWP_BASEPATH . '/libraries'); 

/** Initialize Plugin */
global $wpdb; 
$route = new EAWPCoreRoute(); 
$plugin = new EAWPCorePlugin($wpdb, $route);
$plugin->initialize();

I want to pass on the ID of the current user to Easy!Appointments. In the plug in I add this code:

if(!function_exists('wp_get_current_user')) {
    include(ABSPATH . "wp-includes/pluggable.php"); 
} 

$wp_id = get_current_user_id();

This tells me the current user. That is what I need. Now how do I now pass that on so codeigniter/Easy!Appointments can use it in my controller?

What I have tried:
In my codeigniter controller I have added
require_once( “/path to wp/wp-includes/user.php” );
and then
$wp_id = get_current_user_id();

Which then tells me I am not logged in.

I have also tried adding to the controller
require_once( “/path to wp/wp-includes/pluggable.php” );

and that just kills it.

So, how to I make these WP functions or at least the results of functions available to my codeigniter controller. Do I just make it a global? How?