Right now, we need to figure out what’s preventing programming, because this is a much more fundamental problem than the one with the LEDs.
Again, I would suggest that you actually remove U2 and U3 while debugging this– and do not put them back in –until you are sure that you can get the microcontroller to work normally.
Using both sets of jumpers like you did could potentially damage the microcontroller, but that shouldn’t be an issue since you’ve got the extra chip to try. Are you sure that the extra has the same Arduino bootloader on it?
