*So I'd make a mesh from scratch in the 3d max and then unwrap it and make the diffuse, specular, normal maps in the photoshop for the mesh.

*Then I would import it into milkshape. - Would the unwrap still be fine in milkshape or does it just get reseted etc.?
*If not then what should I do to get the mesh unwraped if I wont be able to do that in 3dmax.

*If the unwrap will be okay and I get the accessory work and get it to CTU, how do I like put all those maps I've done to work with the accessory?

*I've gone through the material replacer tutorials and how to make the mask but since my mesh would be bran new in the CTU, would the proces be different?

The map will be the same in Milkshape, yes. Make sure that you split any seams - that is, any vertices which appear in two different spots on the map need to be unwelded/split.

Import the textures into CTU the same as you would for a simple texture edit - save them as DDS files with the appropriate compression (use the compression of the existing textures as a guide, but generally no alpha = DXT1 compression, with alpha = DXT2 compression), and then replace the EA textures with them. Make sure you go to the designs tab and add a design before replacing the mesh, or you won't be able to add the textures.