So, I've recently started a randomized Rom hack of Sapphire, and my autism is kicking in about things not looking like their typing.
I want my ghost/bug horsea to look like a terrifying arthropod. Well, at least be colored in such a way as to clue me in.
So, I'm looking for a way to do some palette swapping here.

I know about http://artemis251.fobby.net/downloads/emerald/
However, it's for Emerald. I've attempted to force it. Things get weird. For one it swaps my HP and Exp bars. For second, pidgeys become angelic yet horrific beasts of purest pastel and lack of outline. And then there was the Wally having a bad egg issue.

Any other similar utilities available? If not, any idea on how to go about doing this manually?