All similarly coloured items should be considered linked, and should be changed to mirror each other. Although leaving them different will not destroy a map necessarily it may have adverse effects.
Stem - Determines how all the bitmaps are blended and used within the shader. Changing this should rarely be done, and will rarely result in desirable results as each stem needs certain bitmaps, and perhaps certain shader layouts.
Basemap - the basemap is usually the colour bitmap: it will be rendered almost always as-is by the shader: basemap can be considered the Diffuse map.
Unknown [0] [bitm] - The bumpmap for the shader: can be any bitmap type and the engine will try to convert it into a bumpmap: using normal maps results in working bumps in-game. Bump maps ("black & white" or height maps) may work here as well, although that is untested.
Unknown [3] [bitm] - The detail map for the shader: this bitmap will be rendered much smaller then the basemap and will tile within. It is used to give textures more detail when viewed up close.
In all a shader can contain any of the following bitmap types:
Basemap (diffuse map)
Illuminaton map (self-illume map)
Opacity (usually, if not always, contained within the basemap or bumpmap alpha channel)
Bumpmap (usually, if not always, a normal map)
Reflectionmap (Usually a cubemap, also)
Specularity map (Usually, if not always, contained within the basemap or bumpmap alpha channel)
