Figured out the problem, don't know best way of fixing it yet:

With each iteration, the OrderedPairs are keeping the RV that was
created in the previous runthrough of findBestRV(). Because of this,
absurdly high rhyme values are being generated for each runthrough of
the findBestRV() method. This ends up creating a sort of parabola
effect though since there is very little or no extra rhyme value being
added to OrderedPairs at the very bottom. So have to figure out an
efficient way of resetting to the original rhyme value for each ordered
pair with each runthrough.

src/com/shakenearth/Prhymer.java

@@ -20,7 +20,8 @@ public class Prhymer {
 
 	public static void main(String[] args){
 
-		//0 for comparing two words and/or phrases, 1 for finding rhyming words for a specific word or phrase, 2 for a GUI.
+		//0 for comparing two words and/or phrases, 1 for finding rhyming words for a specific word or phrase, 2 for a GUI
+		// and 3 for phoneme comparison.
 		final int TESTING = 2;
 
 		if(TESTING == 0){ //comparing two words and/or phrases

src/com/shakenearth/rhyme_essentials/Node.java

@@ -72,6 +72,8 @@ public void findBestIndexSetAndSendItUp(){
 
 		this.setBestSet(bestSet);
 
+		System.out.println("OLD BEST: " + bestSet);
+
 		if(parentIndexSet != null){
 
 			parentIndexSet.addIndexes(bestSet.getIndexes(), bestSet.getRhymeValueForSet());

src/com/shakenearth/rhyme_essentials/OrderedPair.java

@@ -179,6 +179,7 @@ public void calculateGapPenalty(int lSize) {
 		}
 
 		System.out.println("NEW DEDUCTION: " + deduction);
+		System.out.println("RV BEFORE DEDUCTION: " + getRhymeValue());
 
 		setRhymeValue(getRhymeValue() - deduction);
 

src/com/shakenearth/rhyme_essentials/RhymeFinder.java

@@ -1,7 +1,5 @@
 package com.shakenearth.rhyme_essentials;
 
-import java.io.FileNotFoundException;
-import java.io.PrintWriter;
 import java.nio.charset.*;
 import java.nio.file.*;
 import java.util.*;
@@ -168,45 +166,12 @@ public double newFindRhymePercentileForWords(Word word1, Word word2){
 		//2 - Calculate RVs
 		int echelon = 0;
 		while(cartesianProduct.size() != 0){
-
+			System.out.println("\n\nWHILE LOOP ITERATION: " + cartesianProduct.size());
+			System.out.println("\nCartesian Product: " + cartesianProduct);
 			echelon = cartesianProduct.size() - 1;
-			allRVs.add(findBestRV(cartesianProduct, echelon, new ArrayList<Integer>(), 0, cartesianProduct.size(),
+			allRVs.add(findBestRV(cartesianProduct, echelon, new ArrayList<Integer>(), 0, cartesianProduct.get(echelon).size(),
 					longerWord.getListOfPhonemes().size()));
 
-			//print REF CP:
-			/*int echelonPrint = echelon;
-			for(int i = 0; i < cartesianProduct.size(); i++){
-				
-				ArrayList<OrderedPair> currentRow = cartesianProduct.get(i);
-				
-				for(int j = 0; j < echelonPrint; j++){
-					
-					System.out.print("          ");
-					
-				}
-				
-				for(int j = echelonPrint; j < currentRow.size(); j++){
-					
-					OrderedPair pair = currentRow.get(j);
-					
-					if(pair.getShorterWordPhoneme().length()  == 2 && pair.getLongerWordPhoneme().length()  == 2){
-						
-						System.out.print(pair + "  ");
-						
-					}else if(pair.getShorterWordPhoneme().length()  != pair.getLongerWordPhoneme().length()){
-						
-						System.out.print(pair + "   ");
-						
-					}else if(pair.getShorterWordPhoneme().length()  == 1 && pair.getLongerWordPhoneme().length()  == 1){
-						
-						System.out.print(pair + "    ");
-						
-					}
-					
-				}
-				
-			}*/
-
 			cartesianProduct.remove(0);
 			echelon = 0;
 
@@ -283,21 +248,23 @@ private ArrayList<ArrayList<OrderedPair>> findCartesianProduct(Word word1, Word
 
 	}
 
+
 	private double findBestRV(ArrayList<ArrayList<OrderedPair>> cpMatrix, int echelon, ArrayList<Integer> indexes, 
 			double cumulative, int bound, int lSize){
 
-		ArrayList<OrderedPair> currentRow = cpMatrix.get(echelon); //echelon index number is the same as the current row index.
-
+		ArrayList<OrderedPair> currentRow = cpMatrix.get(echelon); //echelon number is the same as the current row index.
+		System.out.println("CUMULATIVE: " + cumulative);
 		for(int i = echelon; i < bound; i++){
 
-			currentRow.get(i).setRhymeValue(currentRow.get(i).getRhymeValue() + cumulative);;
+			currentRow.get(i).setRhymeValue(currentRow.get(i).getRhymeValue() + cumulative);
 
 		}
 
 		OrderedPair bestPairForRow = null;
 		int indexToAdd = 0;
+		System.out.println("\nECHELON: " + echelon);
+		System.out.println("BOUND: " + bound);
 		for(int i = echelon; i < bound; i++){
-
 			if(i == echelon){
 
 				bestPairForRow = currentRow.get(i);
@@ -322,11 +289,13 @@ private double findBestRV(ArrayList<ArrayList<OrderedPair>> cpMatrix, int echelo
 
 			bestPairForRow.setIndexes(indexes);
 			bestPairForRow.calculateGapPenalty(lSize);
+			System.out.println("ENDS ON: " + bestPairForRow);
 			return bestPairForRow.getRhymeValue();
 
 		}else{
 
 			echelon = echelon - 1;
+			System.out.println("USES: " + bestPairForRow + "\n");
 			return findBestRV(cpMatrix, echelon, indexes, bestPairForRow.getRhymeValue(), indexes.get(indexes.size() - 1), lSize);
 
 		}