Uploading Bootloader Into Empty atmega328

I00 µF rather excessive on the output of the regulator, 0.1µF plus 4.7 µF more than adequate.

1BH62 on reset pin is a fast recovery diode - not actually relevant for this function; any ordinary switching diode is sufficient (and looking at specs, may have lower forward drop). People are inclined to throw around fast recovery or Schottky diodes presuming they are somehow "better" in circuits such as for inductive "flyback" diodes without comprehending what they actually do. A fast recovery diode turns off more quickly than a common signal or (particularly,) power diode but is no different in turning on, so there is no advantage. And the forward voltage drop is of no concern since in this case, the only function of the diode is to prevent the reset voltage approaching the 12V (or so) value which puts it in "high voltage programming" mode.