I was able to successfully resolve this problem by using AttachInterrupt().
Specifically I found a library for IR Remotes that is interrupt based instead of polling based as I was previously trying to use.
In case anyone is interested the finished RFID IR remote control cat feeder code is:
/*** Cord Slatton
* date 12-28-2012 **/
//IR includes
//info: http://www.zbotic.com/index.php/download/
//download: http://www.zbotic.com/index.php/download_file/view/12/118/
#include "PCInterrupt.h"
#include "Device.h"
#include "irController.h"
#define RFID_ENABLE 8 //to RFID ENABLE
#define CODE_LEN 10 //Max length of RFID tag
#define START_BYTE 0x0A
#define STOP_BYTE 0x0D
#define MOTOR_RUN_LENGTH 1000 //time, in ms, to run door motor
char tag[CODE_LEN];
int pwm_b = 11; //PWM control for motor outputs 3 and 4 is on digital pin 11
int dir_b = 13; //direction control for motor outputs 3 and 4 is on digital pin 13
int door_status = 1; // 1 == closed, 0 == open
int manual_mode = 1; // 1 == auto, 0 == manual
//PIR sensor
const int sensorPIR = A0;
//IR init
int manualModePin = 10; //led pin for indication of manual mode
IRController irController;
unsigned long rfidHitTime = 0; //when did we get last rfid hit?
unsigned long pirHitTime = 0; //when did we get last PIR hit?
unsigned long pirClose = 0;
unsigned long rfidClose = 0;
void setup() {
Serial.begin(2400); //parallax rfid reader seems to only like serial 2400
Serial.println("RoboFeeder Online");
//rfid
pinMode(RFID_ENABLE,OUTPUT);
//motor
pinMode(pwm_b, OUTPUT);
pinMode(dir_b, OUTPUT);
//PIR
pinMode(sensorPIR, INPUT);
digitalWrite(sensorPIR, LOW);
Serial.println("Warming up PIR...");
delay(10000);
Serial.println("PIR ready");
//IR remote
pinMode(manualModePin, OUTPUT);
digitalWrite(manualModePin, LOW);
int res = irController.begin(IR_PIN, OTHER_DEVICE);
if (res != SUCCESS) {
Serial.println("error=");
Serial.println(res);
}
Serial.println("IR Remote enabled");
Serial.println("RoboFeeder startup test: Door");
openDoor();
delay(2500);
closeDoor();
Serial.println("RoboFeeder door test complete");
}
void loop() {
delay(1500);
enableRFID();
getRFIDTag(); //waiting function, till gets any tag
disableRFID();
openDoor();
sendCode();
Serial.flush();
clearCode();
}
/*** Clears out the memory space for the tag to 0s. */
void clearCode() {
for(int i=0; i<CODE_LEN; i++) {
tag[i] = 0;
}
}
/*** Sends the tag to the computer. */
void sendCode() {
Serial.print("TAG:");
for(int i=0; i<CODE_LEN; i++) {
Serial.print(tag[i]);
}
Serial.println("\r");
}
/**************************************************************/
/******************** RFID Functions ***********************/
/**************************************************************/
void enableRFID() {
digitalWrite(RFID_ENABLE, LOW);
}
void disableRFID() {
digitalWrite(RFID_ENABLE, HIGH);
}
/*** Blocking function, waits for and gets the RFID tag. */
void getRFIDTag() {
byte next_byte;
while(Serial.available() <= 0) {
if(door_status == 0){ //open
pirDetection();
rfidClose = millis() - rfidHitTime;
pirClose = millis() - pirHitTime;
Serial.print("RFID Close: ");
Serial.print(rfidClose);
Serial.print(" - PIR Close: ");
Serial.println(pirClose);
//if door has been open for more than a certain amount of time with no rfid hit and PIR no hit for certain time
if( (rfidClose > 40000) && (pirClose > 15000) ){
closeDoor();
}
}
IRRemote();
if(manual_mode == 0)
manualMode();
}
//PIR set to current loop time to keep it from freaking out
pirHitTime = millis();
if((next_byte = Serial.read()) == START_BYTE) {
byte bytesread = 0;
while(bytesread < CODE_LEN) {
if(Serial.available() > 0) { //wait for the next byte
if((next_byte = Serial.read()) == STOP_BYTE) break;
tag[bytesread++] = next_byte;
}
}
rfidHitTime = millis(); //keep track of when last rfid hit was
}
}
/**************************************************************/
/******************** Motor Functions ***********************/
/**************************************************************/
void openDoor() {
if(door_status == 1){
motorRun(150);
digitalWrite(dir_b, HIGH); //Set motor direction, 1 low, 2 high
Serial.println("Door opening");
delay(MOTOR_RUN_LENGTH);
motorStop();
door_status = 1 - door_status;
}
}
void closeDoor() {
if(door_status == 0){
motorRun(150);
digitalWrite(dir_b, LOW); //Reverse motor direction, 1 high, 2 low
Serial.println("Door closing");
delay(MOTOR_RUN_LENGTH);
motorStop();
door_status = 1 - door_status;
}
}
void motorRun(int speed) {
analogWrite(pwm_b, speed); //set motor to run at speed variable value
}
void motorStop() {
analogWrite(pwm_b, 0); //set motor to run at 0
}
/**************************************************************/
/******************** PIR Functions ***********************/
/**************************************************************/
boolean pirDetection() {
//returns true if PIR analog reading has been rising for more than 10 cycles,
//false if has been falling
int counter = 0;
int pirSensorReading[10];
int avgReading = 0;
while(counter < 10){
pirSensorReading[counter] = analogRead(sensorPIR);
avgReading += pirSensorReading[counter];
counter++;
delay(300);
}
avgReading = avgReading/10;
Serial.print("Avg. PIR: ");
Serial.print(avgReading);
Serial.print(" - Last PIR: ");
Serial.println( pirSensorReading[9] );
if( (pirSensorReading[9] > avgReading+1) || (analogRead(sensorPIR) > 700) ){
pirHitTime = millis(); //keep track of when last PIR hit was
return true;
}
else if(pirSensorReading[9] <= avgReading){
return false;
}
}
/**************************************************************/
/******************** IR Remote Functions ***********************/
/**************************************************************/
void IRRemote(){
int val = irController.read(); // Returns negative value if no new command rcvd
if (val >=0){
Serial.print("Key: ");
Serial.println(val);
if(val == 100){
manual_mode = 1 - manual_mode;
}
else if( (val >= 0) && (manual_mode == 0) ){
if(door_status == 1)
openDoor();
else
closeDoor();
}
}
delay(500);
}
//blocking function that won't let you leave till you turn off manual mode
void manualMode(){
disableRFID();
Serial.println("Manual Mode on");
digitalWrite(manualModePin, HIGH);
while(manual_mode == 0){
IRRemote();
}
Serial.println("Manual Mode exiting");
digitalWrite(manualModePin, LOW);
//set sensors to count from now, esentially zero them out
pirHitTime = millis();
rfidHitTime = millis();
enableRFID();
}