jjTilesFromTileset accepts an extra parameter for that very purpose, named paletteColorMapping. You want most colors to be mapped to their current color (paletteColorMapping[i] == i), and those that look wrong to be mapped to something else.

If you find that it's more complicated than that, and some colors should be replaced with one color in one context and another in another context, jjPIXELMAP is there to give you a helping hand. The documentation offers an example that already does something quite similar.