After removing the replacing the MCU, a short to pin 4 was cured and selecting the correct board in Arduino cured the pin definition problem. Turns out the MCU was fine, but the short must have been underneath it.

Now it is sitting on a sunny shelve happily beeping every 2 hours and 17 minutes. Only problem now is that it does not seem annoying to me - I actually quite like it! I guess it would be annoying if somebody was trying to sleep though.