ATMega328 functions, but will not output to any pins Problem:
ATMega328 Refuses to digitalWrite() to any pins, I can upload and run sketches using the board UNO from the ide on the 328 and can confirm it is working using the serial monitor (see code).
I am using this FTDI module.
Board Manager -- UNO works, but ATMega328 Doesn't

By using the UNO board under board manager, I am capable of writing sketches and communicating with the 328 just fine. 
But when I use the ATMega328 at 5.5V,16Mhz I receive the following error.
         Using Port                    : COM3

         Using Programmer              : arduino

         Overriding Baud Rate          : 57600

avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x00

avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x00

avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x00

avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0xe0

avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0x00



avrdude done.  Thank you.

Code &amp; Serial Monitor &quot;Proving&quot; it works
I have tried every usable PWM and other pins to attempt to output using LED's, buzzers and even other Arduino's to read inputs but none of the pins will output high when requested.
I believe that Arduino IDE is attempting to compile my code for the UNO and those pins do not work on the ATMega328 but this could be completely incorrect and someone please correct me if this is a wrong assumption.
Lastly, I have been able to use the SCL and SCA pins to communicate with an I2C LED shield.
Does anyone know why I cannot write sketch to the ATMega328 using the FTDI and my configuration.
Posted Below are images and very rough Fritzing schematics of how I am setup.
void setup() {
  Serial.begin(9600);
  pinMode(5,OUTPUT);
}

void loop() {
  Serial.println(&quot;TICK&quot;);
  digitalWrite(5,HIGH);
  delay(1000);
  digitalWrite(5,LOW);
  }


My Breadboard

Fritzing Schematic
This may not be your only problem, but you need a second delay.
void loop() {
  Serial.println(&quot;TICK&quot;);
  digitalWrite(5,HIGH);
  delay(1000);
  digitalWrite(5,LOW);
  delay(1000);    // LOW for a second as well
  }

Otherwise you will not be able to see the LOW part, because it will be really quick.


I believe that Arduino IDE is attempting to compile my code for the UNO and those pins do not work on the ATMega328

The Uno has an Atmega328 on it, and I usually compile for the Uno when uploading to a custom board, so this is not the issue.