Hey, I believe you missed the Sitrus, Pecha, and Chesto Berries in Route 2[I don't remember the exact locations but they are hidden items in the bushes]. Also you can get a Heart Scale in a bush near the Pokemon Groomer on Rt.1
Great job on the 100% guide! I think you missed the part where you can get Scraggy where you first meet Emily in Power Plant, after battling Scarlett at the top of Sky Tower/when the fires stop in Blackview