ATMega328 functions, but will not output to any pins
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.