Glad to hear you figured it out. I just finished adding sound to this game, which helps a lot (for me at least being a musician), plus it's more like the original now. Here's the code:
/*Simon Says game by Robert Spann*/
int switch1 = 11; //The four button input pins
int switch2 = 10;
int switch3 = 9;
int switch4 = 8;
int led1 = 5; //LED pins
int led2 = 4;
int led3 = 3;
int led4 = 2;
int turn = 0;
int speakerPin = 6;
int input1 = LOW;
int input2 = LOW;
int input3 = LOW;
int input4 = LOW;
int randomArray[100]; //Intentionally long to store up to 100 inputs (doubtful anyone will get this far)
int inputArray[100];
void setup() {
Serial.begin(9600);
pinMode(led1, OUTPUT);
pinMode(led2, OUTPUT);
pinMode(led3, OUTPUT);
pinMode(led4, OUTPUT);
pinMode(switch1, INPUT);
pinMode(switch2, INPUT);
pinMode(switch3, INPUT);
pinMode(switch4, INPUT);
pinMode(speakerPin, OUTPUT);
randomSeed(analogRead(0)); //Added to generate "more randomness" with the randomArray for the output function
for (int y=0; y<=1000; y++){ //For statement to loop through the output and input functions
output();
input();
}
}
void output() { //function for generating the array to be matched by the player
for (int y=turn; y <= turn; y++){ //Limited by the turn variable
Serial.println(""); //Some serial output to follow along
Serial.print("Turn: ");
Serial.print(y);
Serial.println("");
randomArray[y] = random(1, 5); //Assigning a random number (1-4) to the randomArray[y], y being the turn count
for (int x=0; x <= turn; x++){
Serial.print(randomArray[x]);
if (randomArray[x] == 1) { //if statements to display the stored values in the array
digitalWrite(led1, HIGH);
playTone(1915, 200); //Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led1, LOW);
delay(100);
}
if (randomArray[x] == 2) {
digitalWrite(led2, HIGH);
playTone(1519, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led2, LOW);
delay(100);
}
if (randomArray[x] == 3) {
digitalWrite(led3, HIGH);
playTone(1275, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led3, LOW);
delay(100);
}
if (randomArray[x] == 4) {
digitalWrite(led4, HIGH);
playTone(956, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led4, LOW);
delay(100);
}
}
}
}
void input() { //Function for allowing user input and checking input against the generated array
for (int x=0; x <= turn;){ //Statement controlled by turn count
input1 = digitalRead(switch1);
input2 = digitalRead(switch2);
input3 = digitalRead(switch3);
input4 = digitalRead(switch4);
if (input1 == HIGH){ //Checking for button push
digitalWrite(led1, HIGH);
playTone(1915, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led1, LOW);
inputArray[x] = 1;
delay(50);
Serial.print(" ");
Serial.print(1);
if (inputArray[x] != randomArray[x]) { //Checks value input by user and checks it against
fail(); //the value in the same spot on the generated array
} //The fail function is called if it does not match
x++;
}
if (input2 == HIGH){
digitalWrite(led2, HIGH);
playTone(1519, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led2, LOW);
inputArray[x] = 2;
delay(50);
Serial.print(" ");
Serial.print(2);
if (inputArray[x] != randomArray[x]) {
fail();
}
x++;
}
if (input3 == HIGH){
digitalWrite(led3, HIGH);
playTone(1275, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led3, LOW);
inputArray[x] = 3;
delay(50);
Serial.print(" ");
Serial.print(3);
if (inputArray[x] != randomArray[x]) {
fail();
}
x++;
}
if (input4 == HIGH){
digitalWrite(led4, HIGH);
playTone(956, 200);//Passes tone value and duration of the tone to the playTone function
delay(200);
digitalWrite(led4, LOW);
inputArray[x] = 4;
delay(50);
Serial.print(" ");
Serial.print(4);
if (inputArray[x] != randomArray[x]) {
fail();
}
x++;
}
}
delay(500);
turn++; //Increments the turn count, also the last action before starting the output function over again
}
void fail() { //Function used if the player fails to match the sequence
playTone(1432, 200); //Tune playing when fail, there is a more elegant way to do this, but this works for short tunes
playTone(1, 5);
playTone(1432, 200);
playTone(1700, 200);
playTone(1275, 200);
playTone(1432, 200);
playTone(1, 5);
playTone(1432, 200);
playTone(1700, 400);
for (int y=0; y<=5; y++){ //Flashes lights for failure
digitalWrite(led1, HIGH);
digitalWrite(led2, HIGH);
digitalWrite(led3, HIGH);
digitalWrite(led4, HIGH);
delay(200);
digitalWrite(led1, LOW);
digitalWrite(led2, LOW);
digitalWrite(led3, LOW);
digitalWrite(led4, LOW);
delay(200);
}
delay(500);
turn = -1; //Resets turn value so the game starts over without need for a reset button
}
void playTone(int tone, int duration) {
for (long i = 0; i < duration * 1000L; i += tone * 2) {
digitalWrite(speakerPin, HIGH);
delayMicroseconds(tone);
digitalWrite(speakerPin, LOW);
delayMicroseconds(tone);
}
}
void loop() { //Unused void loop(), though for some reason it doesn't compile without this /shrug
}
The main thing that was added was the playTone function after the fail function. Don't ask me how it works, as I barely know. I found the following code, and just tried to find the source to give credit but can't seem to figure out exactly where I found it last night.
int speakerPin = 9;
int length = 15; // the number of notes
char notes[] = "cdefgabC "; // a space represents a rest
int beats[] = { 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4 };
int tempo = 300;
void playTone(int tone, int duration) {
for (long i = 0; i < duration * 1000L; i += tone * 2) {
digitalWrite(speakerPin, HIGH);
delayMicroseconds(tone);
digitalWrite(speakerPin, LOW);
delayMicroseconds(tone);
}
}
void playNote(char note, int duration) {
char names[] = { 'c', 'd', 'e', 'f', 'g', 'a', 'b', 'C' };
int tones[] = { 1915, 1700, 1519, 1432, 1275, 1136, 1014, 956, };
// play the tone corresponding to the note name
for (int i = 0; i < 8; i++) {
if (names[i] == note) {
playTone(tones[i], duration);
}
}
}
void setup() {
pinMode(speakerPin, OUTPUT);
}
void loop() {
for (int i = 0; i < length; i++) {
if (notes[i] == ' ') {
delay(beats[i] * tempo); // rest
} else {
playNote(notes[i], beats[i] * tempo);
}
// pause between notes
delay(tempo / 2);
}
}
This code also shows the values for a C scale (scale with all whole steps between notes). The values are stored in the tones array, and called with the names array. This should give you a starting place for creating custom tunes though using the values, as a quick reference:
Low C = 1915
D = 1700
E = 1519
F = 1432
G = 1275
A = 1136
B = 1014
High C = 956
I assume any half steps (such as A#) would be the number in the middle of the two full steps (G and B, (1275+1136)/2 = 1206).
The tune I added into the fail part of the game is the classic "nanny nanny boo boo" type tune. 
I am using a speaker I salvaged from an old computer from my work, but you can buy a small speaker at radio shack that should work just as well, maybe not quite as loud though.
