final working code :D


// Variables for calculating PERIOD and SEX pointers
//float speedPointer();

int encoder[108];
//PROGMEM prog_uchar encoder[106];
//prog_uchar encoder[106] PROGMEM;
//unsigned char lastEncoder0Pos;
int displayRead;
int lastEncoder0Pos;
unsigned char encoder0Pos;
int steps;

int timePeriod=60;
int passedDays=15;
int cycleCount;
int gear20=18;
int gear24=96;
int delayRate;
int pointerPos=0;
//int sexPoint=0;
//int reading[107];
int initialSteps;
int delayMillis;
int savedMillis;
int ellapsedMillis;
int displayEncoder;
//int lastEncoder0Pos;
int lastChange;

//Variables for communicating to Processing
int firstByte; // value for Period
int secondByte; // value for Initial Date
int serialInArray[3]; // array for storing 3 bytes as they arrive from processing
int serialCount = 0; // for counting the number of bytes received

// ENCODER Variables
#define encoder0PinA 2
#define encoder0PinB 3
//volatile int encoder0Pos = 0;

// Stepper Motor Variables
int counter=0;
#include <Stepper.h>
//Motor Steps for Motor 1
#define motor1Steps 24 // change this depending on the number of steps
// Steps fo motor 2
#define motor2Steps 20 // per revolution of your motor
// Pins 4 to 7 for Motor 1
#define motorPin1 8
#define motorPin2 9
#define motorPin3 10
#define motorPin4 11
//Pins 8-11 for Motor 2
#define motorPin5 4
#define motorPin6 5
#define motorPin7 6
#define motorPin8 7
// initialize of the Stepper library:
Stepper myStepper(motor1Steps, motorPin1,motorPin2,motorPin3,motorPin4);
Stepper myStepper2(motor2Steps,motorPin5,motorPin6,motorPin7,motorPin8);

void setup() {
// set the motor speed at 60 RPMS:
myStepper.setSpeed(10);
myStepper2.setSpeed(60);

// Initialize the Serial port:
Serial.begin(9600);
// myStepper.step(10);

//SETUP FOR ENCODER
pinMode(encoder0PinA, INPUT);
digitalWrite(encoder0PinA, HIGH); // turn on pullup resistor
pinMode(encoder0PinB, INPUT);
digitalWrite(encoder0PinB, HIGH); // turn on pullup resistor
attachInterrupt(0, doEncoder, CHANGE); // encoder pin on interrupt 0 - pin 2
Serial.begin (9600);
Serial.println(”start”); // a personal quirk
savedMillis=millis();
initialSteps=-106.67*passedDays/timePeriod;
delayMillis=9.375*timePeriod;
myStepper2.step(int(initialSteps));
Serial.println(initialSteps);
}

void loop() {

/*
if (Serial.available() > 0) {
// read the most recent byte (which will be from 0 to 255)
if(Serial.read()==65){
timePeriod = Serial.read();
passedDays = Serial.read();
}
}
*/
/*
serialInArray[serialCount] = Serial.read(); // read a byte sent by processing
serialCount++; // increment number of bytes received
if (serialCount > 2 ) { // when 3 bytes received
firstByte = serialInArray[1]; // get value for PERIOD
secondByte = serialInArray[2]; // get value for INITIAL DATE
serialCount = 0;
}
*/

// delayMillis=0;
// Serial.println(delayMillis);

ellapsedMillis=millis()-savedMillis;
// Serial.println(ellapsedMillis);
if(ellapsedMillis>=delayMillis){
// save the reading
encoder[pointerPos]=encoder0Pos;
Serial.println(”writingwhenmillis-lastChange>=delayMillis”);
Serial.println(pointerPos);
Serial.println(encoder0Pos, DEC);
//Serial.println(ellapsedMillis);
myStepper2.step(-1);
savedMillis=millis();
pointerPos+=1;
// lastChange = millis();
// if (encoder[pointerPos]>0) {
if(cycleCount>0){
Serial.println(”encoder[pointerPos]”);
Serial.println(encoder[pointerPos],DEC);
Serial.println(encoder0Pos, DEC);

steps=int(0.375*encoder[pointerPos]-0.375*encoder0Pos);
Serial.println(steps);
myStepper.step(steps);
}
/*
// if (millis() - lastChange >= delayMillis*0.8) {
if (millis() - savedMillis >= delayMillis*0.8) {
// save the reading
encoder[pointerPos]=encoder0Pos;
Serial.println(”writingwhenmillis-lastChange>=delayMillis”);
Serial.println(pointerPos);
Serial.println(encoder0Pos, DEC);
//prog_uchar encoder[pointerPos]=lastEncoder0Pos;
}
}
*/
if (pointerPos == 106){
cycleCount+=1;
pointerPos=0;
if (cycleCount==3){
myStepper2.step(3);
}
Serial.println(”cycleCount”);
}
}

}

void doEncoder(){
if (digitalRead(encoder0PinA) == HIGH) { // found a low-to-high on channel A
if (digitalRead(encoder0PinB) == LOW) { // check channel B to see which way
// encoder is turning
encoder0Pos = encoder0Pos - 1; // CCW
}
else {
encoder0Pos = encoder0Pos + 1; // CW
}
}
else // found a high-to-low on channel A
{
if (digitalRead(encoder0PinB) == LOW) { // check channel B to see which way
// encoder is turning
encoder0Pos = encoder0Pos + 1; // CW
}
else {
encoder0Pos = encoder0Pos - 1; // CCW
}
}

if(encoder0Pos>64){
encoder0Pos=1;
}
if(encoder0Pos<1){
encoder0Pos=64;
}
// Serial.println (encoder0Pos, DEC); // debug - remember to comment out
}