Yes the base sprites are coming from the in game folder. In your Reborn folder, go to Graphics, then Battlers, then pick the respective pokemon's number. For the recoloring purposes start with the NORMAL sprite, not the shiny one and make alterations from there. Also be sure to save them as .png files and 160x160 pixels.
Amethyst is a very busy woman, and has a lot on her plate, so I can't blame her for not having time for each and every thing. If you do have questions, as I said there are plenty of people you can ask, but for the more generic ones, I try to keep that FAQ I linked to relatively up to date.