Now with the fixed animation you just made in Photoshop/grabbed from Pokemon Showdown you'll probably also need the shiny alternative. I tend to just grab the rips on the serebii dex:
http://www.serebii.net/pokedex-xy/
The quality of some Serebii rips is really bad but the colours are close enough. Save the shiny you want on your computer so that you can open it.
Download and run Aseprite, open the fixed front, fixed back, and the serebii rip.
Now for your Serebii sample you'll need to change one key feature, with the serebii rip open go to the toolbar at the top and click
Sprite >
Color Mode >
Indexed (No Dithering)
Now on the right toolbar go click the eraser and chose the eyedropper instead. Then near the top left of the screen above all the squares of colour click the
Edit Palette button. The edit palette window is your friend use it wisely.
Here is the part where you have a bit of artistic freedom. Zoom in with the mouse wheel and compare the Serebii shiny rip with the animated front, grab an appropriate colour from the shiny, click
Copy on the palette editor, then go to the animated sprite. Find the appropriate colour with the eyedropper again and click
Paste on the palette editor to replace the corresponding colour. Now go to the back and using some artistic liberty replace the corresponding colour.
Now keep doing this and you'll probably have a good front, sometimes the backs have more or different colours. You'll have to wing it in the Palette Editor. Use the RGB or HSB mode and play with the sliders to find a good replacement colour that is about the same as it was originally. This takes a bit more trial and error. HSB option is your friend, use it well.
Once they are done and look fine SAVE AS and upload everything you touched so I can add it to PS.