Once the Arduino powers on, the LED lights up successfully for three seconds before powering off, and never turning on again regardless of the delay values I input into the program.
I don't see a current limit resistor for the LED.
Hmmm. You don't suppose that is because you have it connected to pin 1 of the Arduino instead of pin 2? This is the Tx pin, activated while Optiboot waits to see if you want to program it, then shuts off until you activate the serial interface. I do.