The gallic ships will done after i'm finished with the rest of the ships. The gallic ships use the same colorization stuff as the bretonia and kusari ships (and the liberty logo on caps). I found a way to get some decent results, but it takes quite some time sometimes. For the ones who are trying themselves;
In milkshape you hit the "diffuse" button in the third tab (where you link the textures to the model parts). A new window will pop up showing certain color settings. Red, Blue and Green are the most important ones for this. Normal textures that don't have extra colorization have R: 53, B: 53, G: 53 i believe. Could also be 93 (i don't have milkshape with me to check).
In any case, remember those color settings. Get your hands on some tool to convert .dds files to .tga (or other picture files like jpg, png, psd etc). Convert the textures that need recoloring, open them in photoshop. Add a new layer, fill the new layer with the color settings you found in milkshape. You need to blend the new layer, (liberty, kusari and bretonia ships got the best result with "Multiply", but this doesn't work on all textures (as you can see with the liberty super transport, which is too red)). Next you play with opacity and fill settings a bit. I believe i used 90% on both for the bretonia, kusari and liberty shipline. After this you save the new texture to a seperate file (i advise to use the same name as the one in milkshape, "Lib1d" for example, this will link to the model part called "Liberty 1D" (meaning it's a bit Darker then the regular liberty 1 texture). After this you convert it back to .dds (not necessary when the files are already in .tga) and you link the newly made texture to the model part in milkshape. Note that the model itself will change color in milkshape, this is because the colorization settings get added the already colored texture. Don't mind these changes, it'll all work out once you render them in 3ds max.