Okay, well I just went ahead and fixed up all of the coloring mistakes I could find in the tile set. Apparently there are even some bigger ones that I never noticed before, such as a frame of shooting from a wall jump where X's armored buster was colored red instead of white!Here is a link to the IPS patch.
Here are some examples of things I fixed:
First, a zoomed in view to make it clear where the kneecap uses the brown instead of dark red:
Since X1 has that palette entry as white (I don't know why, but X's palette has two identical shades of white in X1. Maybe the armor white and the eyes were intended to be different shades at one point in X1's development?), I think perhaps originally during development they used the X1 palette for the armor, but then since they realized that white was redundant, they changed one to make the reds look better. Unfortunately the graphic artist did a sloppy job of it, since random frames have his hand or kneecaps using the brown shade still instead of the unique dark red. The first double buster shot frame also had the corner of his arm graphic with a single brown pixel on the white armor part.
This also extends to the charge palette which has the dark red become pure white, which is a leftover from X1's charging palettes, since they clearly didn't correct the red for that palette. I did, however, and it looks all the better for it.
Here are some before and after examples of what I have done:
This also shows that red colored buster tile that I fixed, as well as showcasing how messed up his color scheme was both in graphics and in palette, since the original charging palette clearly shows where they used the brown instead of the red, as the dark red is white, which looks terrible anyway.
Also, the palettes when X is getting armor from Light's capsules had the white for the dark red, since they were just ported from X1, so not only did I fix that, but I also updated those palettes to have a smoother transition to each color, so it's superior to the original versions (the purple was originally too dark, so it kind of just flashes to bright green from that. Now it's a smooth glow):
Improved and fixed version:
You can really tell in the blue areas.
I hope you're willing to use these graphical corrections in your hack, just as a little bonus.