It looks like you missed the pokemon available in the underground railnet available from the Peridot Ward at the very start of the game, with Woobat and Noibat.
Edit: There are also a few items you missed, though I'm not sure if you intend the guide to include these. There is both a common candy and a blue shard to the left of the area where you first fight Fern, a potion in the first alleyway, leftmost box, and a repel in the second alleyway, in a bag to the left.