Solid high light on PIR

So I just set up a board with a pir and range finder. I have both of them working and outputting to my computer. However the red(high) light for the pir only stays on as long as there is motion. I want it to stay on as long as the arduino recognizes motion (5000) after last motion here is the code I would love any help you can give.

int calibrationTime = 30;        //the time we give the sensor to calibrate (10-60 secs according to the datasheet)
long unsigned int lowIn;         //the time when the sensor outputs a low impulse
long unsigned int pause = 5000;  //the amount of milliseconds the sensor has to be low before we assume all motion has stopped
boolean lockLow = true;
boolean takeLowTime;  
int pirPin = 8;                  //the digital pin connected to the Motion Sensor Output
int ledPin = 13;                 //LED pin to denote movement
int ledPin2 = 2;                 //LED pin to denote movement
int pingPin = 12;                //the digital pin connected to the range finder
void setup(){
  Serial.begin(9600);
  pinMode(pirPin, INPUT);
  pinMode(ledPin, OUTPUT);
  pinMode(ledPin2, OUTPUT);
  digitalWrite(pirPin, LOW);
  Serial.print("calibrating sensor ");//give the sensor some time to calibrate
    for(int i = 0; i < calibrationTime; i++){
      Serial.print(".");
      delay(1000);
      }
    Serial.println(" done");
    Serial.println("SENSOR ACTIVE");
    delay(50);
  }

void loop(){

   long duration, inches, cm;   // establish variables for duration of the ping, and the distance result in inches and centimeters
     if(digitalRead(pirPin) == HIGH){
       digitalWrite(ledPin2, LOW);   //the led visualizes the sensors output pin state
       digitalWrite(ledPin, HIGH);   //the led visualizes the sensors output pin state
       if(lockLow){           //makes sure we wait for a transition to LOW before any further output is made:
         lockLow = false;            
         Serial.println("---");
         Serial.print("motion detected at ");
         Serial.print(millis()/1000);
         Serial.println(" sec"); 
         delay(50);
         }         
         takeLowTime = true;
       }

     if(digitalRead(pirPin) == LOW){       
       digitalWrite(ledPin2, HIGH);  //the led visualizes the sensors output pin state
       digitalWrite(ledPin, LOW);  //the led visualizes the sensors output pin state

       if(takeLowTime){
        lowIn = millis();          //save the time of the transition from high to LOW
        takeLowTime = false;       //make sure this is only done at the start of a LOW phase
        }

       if(!lockLow && millis() - lowIn > pause){  
           //makes sure this block of code is only executed again after a new motion sequence has been detected
           lockLow = true;                        
           Serial.print("motion ended at ");      //output
           Serial.print((millis() - pause)/1000);
           Serial.println(" sec");
           delay(50);
           }
       }
      pinMode(pingPin, OUTPUT);
  digitalWrite(pingPin, LOW);   // The PING))) is triggered by a HIGH pulse of 2 or more microseconds.
  delayMicroseconds(200);           // Give a short LOW pulse beforehand to ensure a clean HIGH pulse:
  digitalWrite(pingPin, HIGH);
  delayMicroseconds(500);
  digitalWrite(pingPin, LOW);

  // The same pin is used to read the signal from the PING))): a HIGH
  // pulse whose duration is the time (in microseconds) from the sending
  // of the ping to the reception of its echo off of an object.
  pinMode(pingPin, INPUT);
  duration = pulseIn(pingPin, HIGH);

  // convert the time into a distance
  inches = microsecondsToInches(duration);
  cm = microsecondsToCentimeters(duration);
  
  Serial.print(inches);
  Serial.print("in, ");
  Serial.print(cm);
  Serial.print("cm");
  Serial.println();
  
  delay(1000);
}

long microsecondsToInches(long microseconds)
{
  // According to Parallax's datasheet for the PING))), there are
  // 73.746 microseconds per inch (i.e. sound travels at 1130 feet per
  // second).  This gives the distance travelled by the ping, outbound
  // and return, so we divide by 2 to get the distance of the obstacle.
  // See: http://www.parallax.com/dl/docs/prod/acc/28015-PING-v1.3.pdf
  return microseconds / 74 / 2;
}

long microsecondsToCentimeters(long microseconds)
{
  // The speed of sound is 340 m/s or 29 microseconds per centimeter.
  // The ping travels out and back, so to find the distance of the
  // object we take half of the distance travelled.
  return microseconds / 29 / 2;
}

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However the red(high) light for the pir only stays on as long as there is motion. I want it to stay on as long as the arduino recognizes motion (5000) after last motion

The red light stays on as long as there is motion. And, you want it to stay on as long as there is motion. OK. So, what is the problem?

Ok it stays on as long is there is motion. However if there isnt motion for a couple seconds the arduino still reads it as high. The red light however cuts off. What I want is as long as it is still reading as high I want the red light on.

long unsigned int lowIn;         //the time when the sensor outputs a low impulse
long unsigned int pause = 5000;  //the amount of milliseconds the sensor has to be low before we assume all motion has stopped

This is the delay to keep it at high.

However if there isnt motion for a couple seconds the arduino still reads it as high

How are you determining that? By that state of the on-board LED?

Which PIR are you using?

Well I have an led installed but by that led yes. Im not sure it was a cheap one from radioshack

I don't see any problems in the Sketch you posted. I suggest writing a very simple Sketch that just outputs the state of the PIR.