Haven't been able to look into it quite yet, but maybe you could try to use Mode4 to fix some of the palette problems?
I have no idea how exactly it is supposed to be used (I suspect it uses Conditions) but it apparently deals with patching palettes. There is even a function that apparently takes in 5-bit color values.
I have no idea how exactly it is supposed to be used (I suspect it uses Conditions) but it apparently deals with patching palettes. There is even a function that apparently takes in 5-bit color values.
;PaletteX = c31,31,31 ;X:0~15, cR,G,B (0~31)