Oh editing the Chibi sets is hard because it has a lot of details. Which is why I am making my custom ones, so I can use 4 colors at most. I have done it in the past, and they don't look so bad (there's not gradients, shadows or such, so they're like 3/10 from POV), but what I did was used the body of the RM2k and I want to do everything including the templates and use my own colors wheel.
Try http://piskelapp.com/ because it also animates the sprites so you can see in Real time if the animations suck or not. It's a web browser but you can also download it.