Okay I figured this out!
The problem was actually with where I was defining the pins. They where withing the if statement for the DHT warning. I have moved them outside that statement and it seems to be working fine.
/**
 * The MySensors Arduino library handles the wireless radio link and protocol
 * between your home built sensors/actuators and HA controller of choice.
 * The sensors forms a self healing radio network with optional repeaters. Each
 * repeater and gateway builds a routing tables in EEPROM which keeps track of the
 * network topology allowing messages to be routed to nodes.
 *
 * Created by Henrik Ekblad <henrik.ekblad@mysensors.org>
 * Copyright (C) 2013-2015 Sensnology AB
 * Full contributor list: https://github.com/mysensors/Arduino/graphs/contributors
 *
 * Documentation: http://www.mysensors.org
 * Support Forum: http://forum.mysensors.org
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * version 2 as published by the Free Software Foundation.
 *
 *******************************
 *
 * REVISION HISTORY
 * Version 1.0 - Henrik Ekblad
 *
 * DESCRIPTION
 * Motion Sensor example using HC-SR501
 * http://www.mysensors.org/build/motion
 *
 */
// Enable debug prints
#define MY_DEBUG
#define MY_NODE_ID 233
#define MY_PARENT_NODE_ID 0
#define MY_PARENT_NODE_IS_STATIC
// Enable and select radio type attached
#define MY_RADIO_NRF24
//#define MY_RADIO_RFM69
#include <MySensors.h>
#include <SPI.h>
#include <DHT.h>
#include <Bounce2.h>
unsigned long SLEEP_TIME = 120000; // Sleep time between reports (in milliseconds)
#define DIGITAL_INPUT_SENSOR 2   // The digital input you attached your motion sensor.  (Only 2 and 3 generates interrupt!)
#define DIGITAL_INPUT_SENSOR2 3 // The input for door sensor
#define CHILD_ID_MOTION 1   // Id of the sensor child
#define CHILD_ID_HUM 2
#define CHILD_ID_TEMP 3
#define CHILD_ID_DOOR 4
// Set this to the pin you connected the DHT's data pin to
#define DHT_DATA_PIN 4
// Set this offset if the sensor has a permanent small offset to the real temperatures
#define SENSOR_TEMP_OFFSET 0
// Force sending an update of the temperature after n sensor reads, so a controller showing the
// timestamp of the last update doesn't show something like 3 hours in the unlikely case, that
// the value didn't change since;
// i.e. the sensor would force sending an update every UPDATE_INTERVAL*FORCE_UPDATE_N_READS [ms]
static const uint8_t FORCE_UPDATE_N_READS = 10;
float lastTemp;
float lastHum;
uint8_t nNoUpdatesTemp;
uint8_t nNoUpdatesHum;
bool metric = true;
MyMessage msgHum(CHILD_ID_HUM, V_HUM);
MyMessage msgTemp(CHILD_ID_TEMP, V_TEMP);
// Initialize motion message
MyMessage msg(CHILD_ID_MOTION, V_TRIPPED);
MyMessage msgDoor(CHILD_ID_DOOR, V_TRIPPED);
DHT dht;
void presentation()  
{ 
  // Send the sketch version information to the gateway
  sendSketchInfo("TemperatureAndHumidity", "1.1");
  // Register all sensors to gw (they will be created as child devices)
  present(CHILD_ID_HUM, S_HUM);
  present(CHILD_ID_TEMP, S_TEMP);
  present(CHILD_ID_MOTION, S_MOTION);
  present(CHILD_ID_DOOR, S_DOOR); 
  metric = getControllerConfig().isMetric;
}
void setup()
{
  dht.setup(DHT_DATA_PIN); // set data pin of DHT sensor
  if (1200000 <= dht.getMinimumSamplingPeriod()) {
    Serial.println("Warning: UPDATE_INTERVAL is smaller than supported by the sensor!");
  }
  // Sleep for the time of the minimum sampling period to give the sensor time to power up
  // (otherwise, timeout errors might occure for the first reading)
  sleep(dht.getMinimumSamplingPeriod());
  pinMode(DIGITAL_INPUT_SENSOR, INPUT);      // sets the motion sensor digital pin as input
  pinMode(DIGITAL_INPUT_SENSOR2, INPUT);      // sets the door sensor digital pin as input
  digitalWrite(DIGITAL_INPUT_SENSOR2,HIGH);   // Activate internal pull-up
}
void loop()      
{  
  // Force reading sensor, so it works also after sleep()
  dht.readSensor(true);
  // Get temperature from DHT library
  float temperature = dht.getTemperature();
  if (isnan(temperature)) {
    Serial.println("Failed reading temperature from DHT!");
  } else if (temperature != lastTemp || nNoUpdatesTemp == FORCE_UPDATE_N_READS) {
    // Only send temperature if it changed since the last measurement or if we didn't send an update for n times
    lastTemp = temperature;
    if (!metric) {
      temperature = dht.toFahrenheit(temperature);
    }
    // Reset no updates counter
    nNoUpdatesTemp = 0;
    temperature += SENSOR_TEMP_OFFSET;
    send(msgTemp.set(temperature, 1));
    #ifdef MY_DEBUG
    Serial.print("T: ");
    Serial.println(temperature);
    #endif
  } else {
    // Increase no update counter if the temperature stayed the same
    nNoUpdatesTemp++;
  }
  // Get humidity from DHT library
  float humidity = dht.getHumidity();
  if (isnan(humidity)) {
    Serial.println("Failed reading humidity from DHT");
  } else if (humidity != lastHum || nNoUpdatesHum == FORCE_UPDATE_N_READS) {
    // Only send humidity if it changed since the last measurement or if we didn't send an update for n times
    lastHum = humidity;
    // Reset no updates counter
    nNoUpdatesHum = 0;
    send(msgHum.set(humidity, 1));
    #ifdef MY_DEBUG
    Serial.print("H: ");
    Serial.println(humidity);
    #endif
  } else {
    // Increase no update counter if the humidity stayed the same
    nNoUpdatesHum++;
  }
  // Read digital motion value
    bool tripped = digitalRead(DIGITAL_INPUT_SENSOR) == HIGH;
    Serial.println(tripped);
    send(msg.set(tripped?"1":"0"));  // Send tripped value to gw
    
  // Read digital door value
    bool tripped2 = digitalRead(DIGITAL_INPUT_SENSOR2) == HIGH;
    Serial.println(tripped2);
    send(msgDoor.set(tripped2?"1":"0"));  // Send tripped value to gw
  // Sleep until interrupt comes in on motion sensor. Send update every two minute.
  sleep(digitalPinToInterrupt(DIGITAL_INPUT_SENSOR), CHANGE, digitalPinToInterrupt(DIGITAL_INPUT_SENSOR2), CHANGE, SLEEP_TIME); 
}
Thanks again for all your help everyone!