Atmega328 not Working in Circuit SOLVED!

This may be a lot for you 9V battery. In general 9V batteries are not a desirable energy source.
Also, crystal circuits can be finicky circuits, susceptible to poor layout and noise. Usually you cannot measure the crystal with a multimeter due to loading.

I suggest,

  • Disconnect the LED's and run the "blink without delay". Monitor the "blinking Pin" with your meter.
  • Power with an adapter, either 5V or 12V.