Hey dude. Sorry for the late response. I had a long hiatus because I had a couple of time consuming and unfortunate events that occurred, haha. But now I'm back. I basically used Pokedex Order Editor. It was the most time consuming process ever because I had to keep track of every Pokemon that I ordered already. If two Pokemon gets assigned the same number, #000 in the Pokedex will appear. Those 000s that you might have seen were due to giving a Pokemon the same number as another.