I'm sure this can be simplified. Need some advice.

CheesesController.php

<?php
/**
 * index method
 * @param int $limit The total to return
 * @param int $page The page to pull
 * @return void
 */
	public function index($limit = 25, $page = 1) {
		$this->Cheese->recursive = -1;

		//Fix the pager. It won't pull page if it's not last in the url stack
		$page = 1;
		if(!empty($this->params->named['page'])){
			$page = $this->params->named['page'];
		}else{
			$page = $this->params->paging['page'];
		}

		//Parse the search query
		$this->request->params['named']['query'] = $this->parseSearchQuery();

		$paginationResult = $this->processSearchInformation(
			$limit, 
			array(), 
			array(
				'page' => $page
			)
		);
		$results = $this->Paginator->paginate();
		$this->set('_serialize', 'results');
		$this->set(compact('results'));

		//Fill in the search form
		if(!empty($this->params->query['data'])){
			$this->request->data = $this->params->query['data'];
		}

		//Set the filter options
		$this->setCheeseFilterData();

		$totalCheeseCount = Cache::read('total_cheese_count', 'minutes');
		if(empty($totalCheeseCount)){
			$totalCheeseCount = $this->Cheese->find('count', array('conditions'=>array('Cheese.active'=>1)));
			Cache::write('total_cheese_count', $totalCheeseCount, 'minutes');
		}

		$trendingCheeses = Cache::read('trending_cheeses', 'hour');
		if(empty($trendingCheeses)){
			$trendingCheeses = $this->Cheese->getTrending(5);
			Cache::write('trending_cheeses', $trendingCheeses, 'hour');
		}

		$trendingProducers = Cache::read('trending_producers', 'hour');
		if(empty($trendingProducers)){
			$trendingProducers = $this->Cheese->CheeseProducer->getTrending(5);
			Cache::write('trending_producers', $trendingProducers, 'hour');
		}
		$this->set(compact('totalCheeseCount','trendingProducers','trendingCheeses'));
	}
	
/**
 * processSearchInformation method
 * Handles setting the conditions for the paginate. The conditions are tricky because of the filters (hence the large amount of code).
 * @param int $limit Total results to return
 * @param int $removeIds Items to ignore
 * @param array $options The optioms of model/model_id
 * @param array $condtions Extra conditions that should be concatenated onto the main search conditions
 * @return array The pagination results for the paginate method
 */
	public function processSearchInformation($limit = 25, $removeIds = array(), $options = array(), $conditions = array()){
		$default_options = array(
			'model' => '',
			'model_id' => '',
			'active' => 1,
			'page' => 1
		);
		$options = Set::merge($default_options,$options);

		//IMPORTANT: Set the filter variables
		$this->initializeFilters();

		//$userIp = $this->request->clientIp();
		//Parse the filter string information and get the conditions
		$filterConditions = $this->Filter->getConditions();

		//Certain records require joins in order to process, this method takes care of those.
		$filterConditions = $this->applyFilterJoinConditions($options, $filterConditions);

		//Parse the filter data
		if( !empty($filterConditions) ){

			//Make sure that the query is passed along
			if(!empty($this->passedArgs['query'])){
				$newFilterData = array('AND' => $filterConditions);
				$filterConditions = array_merge($newFilterData, $this->Cheese->parseCriteria($this->passedArgs));
			}else{
				$filterConditions = array_merge($filterConditions, $this->Cheese->parseCriteria($this->passedArgs));
			}

			$this->Paginator->settings['conditions'] = $filterConditions;
		}else{
			//Do search
			$this->Prg->commonProcess();
			$this->Paginator->settings['conditions'] = $this->Cheese->parseCriteria($this->Prg->parsedParams());
		}

		//Make sure that the cheese producer id is passed to the conditions array
		if($options['model'] == 'CheeseProducer' && !empty($options['model_id'])){
			$this->Paginator->settings['conditions']['AND'][] = array('Cheese.cheese_producer_id' => intval($options['model_id']));
		}
		$this->Paginator->settings['conditions']['AND'][] = array('Cheese.active' => $options['active']);

		//Merge any extra conditions that were passed
		if( !empty($conditions) ){
			//$this->Paginator->settings['conditions']['AND'] = array_merge($this->Paginator->settings['conditions']['AND'], $conditions);
			$this->Paginator->settings['conditions']['AND'][] = $conditions;
		}

		//Make sure the conditions array doesn't contain certain records
		if($removeIds){
			$this->Paginator->settings['conditions']['NOT'][] = array('Cheese.id' => $removeIds);
		}

		//Apply the processed conditions to the actual pagination condition array
		$this->Filter->setPaginate('conditions', $this->Paginator->settings['conditions']);

		$this->Paginator->settings['order'] = array(
			'Cheese.created' => 'DESC',
			'Cheese.staff_score' => 'DESC',
			'Cheese.score' => 'DESC'
		);
		$this->Filter->setPaginate('order', $this->Paginator->settings['order']); // optional
		$this->Filter->setPaginate('limit', $limit); // optional
		$this->Paginator->settings['contain'] = array(
				'Attachment' => array(
					'fields' => array('id','path_small','path_med','path_med_crop','path_small_crop')
				),
				'CheeseProducer' => array(
					'fields' => array('id','name')
				),
				'User' => array(
					'fields' => array('id','name','username','email','profile_image_url','attachment_id'),
					'Attachment'
				),
				'CheeseRegion' => array('fields' => array('id','name')),
				'CheeseLocation' => array(
					'Country' => array('fields' => array('name','code')),
					'StateRegion' => array('fields' => array('name','code'))
				),
				'MilkSource' => array(
					'fields' => array('id','name'),
					'Attachment' => array('fields' => array('id','path_small'))
				),
				'MilkTreatment' => array('fields'=>array('id','name')),
				'RennetType' => array(
					'fields'=>array('id','name')
				),
				'Rind' => array('fields'=>array('id','name')),
				'AnimalBreed' => array('fields'=>array('id','name')),
				'Texture' => array('fields'=>array('id','name'))
			);
		$this->Filter->setPaginate('contain', $this->Paginator->settings['contain']);
		
		$this->Paginator->settings['limit'] = $limit;
		$this->Paginator->settings['page'] = $options['page'];
		
		debug($this->Paginator->settings);
		return $this->Paginator->settings;
	}
	
/**
 * applyFilterJoinConditions method
 * Apply any join conditions that need to be added to the main conditions array. 
 * @param array options Some basic record options
 * @param array $filterConditions The data that was return by the filter plugin
 * @return array The joins used by the search conditions (pass along to the main conditions array)
 */
	protected function applyFilterJoinConditions($options = array(), $filterConditions = array()){
		$searchJoins = array();
		$this->Paginator->settings['joins'] = array();

		if($options['model'] == 'Place'){
			//Check to see if a place was passed
			if(!empty($options['model_id'])){
				$searchJoins[] = array(
					'table' => 'cheeses_places',
					'alias' => 'CheesesPlaces',
					'type' => 'INNER',
					'conditions' => array(
						'Cheese.id = CheesesPlaces.cheese_id',
					)
				);
				$searchJoins[] = array(
					'table' => 'places',
					'alias' => 'Place',
					'type' => 'INNER',
					'conditions' => array(
						'CheesesPlaces.place_id = Place.id',
						'CheesesPlaces.place_id' => intval($options['model_id'])
					)
				);
			}
		}

		if(!empty($filterConditions)){
			//Search milk sources
			if(!empty($filterConditions['MilkSource.id ='])){
				$milkSourceId = $filterConditions['MilkSource.id ='];
				unset($filterConditions['MilkSource.id =']);
				//Add a join to search for the milk_source_id
				$searchJoins[] = array(
					'table' => 'cheeses_milk_sources',
					'alias' => 'CheesesMilkSource',
					'type' => 'INNER',
					'conditions' => array(
						'Cheese.id = CheesesMilkSource.cheese_id',
					)
				);
				$searchJoins[] = array(
					'table' => 'milk_sources',
					'alias' => 'MilkSource',
					'type' => 'INNER',
					'conditions' => array(
						'CheesesMilkSource.milk_source_id = MilkSource.id',
						'CheesesMilkSource.milk_source_id' => $milkSourceId
					)
				);
			}

			//Do a search to see what cheese locations have the state_region_id and country_id if found
			if(!empty($filterConditions['CheeseLocation.state_region_id ='])){
				$stateRegionId = $filterConditions['CheeseLocation.state_region_id ='];
				unset($filterConditions['CheeseLocation.state_region_id =']);
				//Add a join to search
				$searchJoins[] = array(
					'table' => 'cheese_locations',
					'alias' => 'CheeseLocation',
					'type' => 'INNER',
					'conditions' => array(
						'CheeseLocation.cheese_id = Cheese.id',
						'CheeseLocation.state_region_id' => $stateRegionId
					)
				);
			}
			//
			if(!empty($filterConditions['CheeseLocation.country_id ='])){
				$countryId = $filterConditions['CheeseLocation.country_id ='];
				unset($filterConditions['CheeseLocation.country_id =']);
				//Add a join to search
				$searchJoins[] = array(
					'table' => 'cheese_locations',
					'alias' => 'CheeseLocation',
					'type' => 'INNER',
					'conditions' => array(
						'CheeseLocation.cheese_id = Cheese.id',
						'CheeseLocation.country_id' => $countryId
					)
				);
			}
		}

		//Set the joins
		if(!empty($searchJoins)){
			$this->Filter->setPaginate('joins', $searchJoins);
			$this->Paginator->settings['joins'] = $searchJoins;
		}

		return $filterConditions;
	}

/**
 * initializeFilters method
 * This sets up the filter variables used by the plugin
 * @param void
 * @return void
 */
	public function initializeFilters(){
		$stateList = Cache::read('active_cheese_state_list','month');
		if(empty($stateList)){
			$stateList = $this->Cheese->CheeseLocation->getActiveStates();
			Cache::write('active_cheese_state_list', $stateList, 'month');
		}

		$countryList = Cache::read('active_cheese_country_list','month');
		if(empty($countryList)){
			$countryList = $this->Cheese->CheeseLocation->getActiveCountries();
			Cache::write('active_cheese_country_list', $countryList, 'month');
		}

		// Add filter
		$this->Filter->addFilters(
			array(
				'milkSource' => array(
					'MilkSource.id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'milkTreatment' => array(
					'Cheese.milk_treatment_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'year' => array(
					'Cheese.year_produced' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'texture' => array(
					'Cheese.texture_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'rennetType' => array(
					'Cheese.rennet_type_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'rind' => array(
					'Cheese.rind_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				),
				'stateRegion' => array(
					'CheeseLocation.state_region_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						),
						'select' => $this->Filter->select('StateRegion',$stateList)
					)
				),
				'country' => array(
					'CheeseLocation.country_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						),
						'select' => $this->Filter->select('Country',$countryList)
					)
				),
				/*'cheeseProducer' => array(
					'Cheese.cheese_producer_id' => array(
						'operator' => '=',
						'value' => array(
							'before' => '', // optional
							'after'  => ''  // optional
						)
					)
				)*/
			)
		);
		unset($countryList,$stateList);
	}
	
	
/**
 * parseSearchQuery method
 * Handles cleaning up the search query
 * @param void
 * @return array
 */
	public function parseSearchQuery(){

		//Make sure the query isn't spaces
		if( !empty($this->params->named['query']) ){
			$this->request->params['named']['query'] = addslashes(trim($this->params->named['query']));
		}else{
			$this->request->params['named']['query'] = '';
		}

		if($this->request->is('post')){
			if(isset($this->request->data['Cheese']['query'])){
				$this->request->params['named']['query'] = $this->request->data['Cheese']['query'];
			}
		}
		return $this->request->params['named']['query'];
	}