I made my first mesh which is really exciting, but I'm having trouble with the texture now. You can still see the part where the buttons were on the original skirt. I've edited the alpha and the overlay and the specular files and it's still there

That's on the mesh bumpmap, which defines the appearance of raised and lowered areas - in this case the buttons. The bumpmap is a dds texture that's linked in the mesh itself so it's handled a little differently. You have two options to fix it:

Use a blank bumpmap. In CTU, when you import your custom mesh in the Meshes tab, scroll down to the bottom of that screen to the Bump Map field. Select the blank bumpmap I've attached.

If you want to edit the original skirt bumpmap, look for the TGI key of the NormalMap at the top of the same screen in the Meshes tab. (Bumpmap and NormalMap are the same thing.) Extract the skirt textures or look in the textures if you already extracted them, and find the .dds with the same number as the last part of the key. For the skirt I think you cloned the file name is afBottomSkirtShort__0x8313bcc09b255461.dds. Edit that texture to remove the buttons. However, editing a bumpmap can be difficult since you have to edit the RGB and the alpha channels separately. Then import your modified bumpmap along with your mesh as described above.

Thank you so much! <3 I edited the skirt's bumpmap in PS because I like the line going down the side and it worked like a charm!

I do have another small issue though, if you wouldn't mind helping. There was a line around a lower part of the skirt where the original texture ended which I thought was part of the bumpmap, but after editing the bumpmap I realised that it wasn't. I tried some different patterns on the mesh and you can see really well on the houndstooth that the bottom part of the skirt where the original was runs fine, but where I've extended it is warped upwards. I checked it out in Milkshape and you can see the problem clearly with the textured version of the mesh (which I didn't really pay attention to since I'm a newb to meshing, haha), but on the smooth and wired version of the meshes, it isn't apparent so I'm not sure what to change in order to fix it

You mean the mismatch across the tummy where the top of the original skirt was? That's caused by the UV mapping of the mesh - the map of where each mesh vertex falls on the textures or how the texture is mapped onto the mesh, however you want to look at it. In Milkshape, after you assign a texture, you can go to the Window menu and click Texture Coordinate Editor and you'll get a window showing the mesh mapped over the texture. You can select and move vertices on that map.

Here's the UV map of the original short skirt mesh:



The gray area is where the original skirt part is on the mesh. You can see there's a gap between the skirt and the skin above the skirt. You (I assume) extended the skirt up using the textures, but since the skin and skirt were mapped separately they don't match up at that line.

You can try moving the vertices of the stomach on the UV map so they line up better with the rest of the skirt. As you work, you can click the main Milkshape window to update the view and see how it looks.

Ahh, that makes sense, thank you so much! I have one more (I really really hope) issue. When I click into the Texture Coordinate Editor, it comes up blank. I tried some different things like selecting the mesh and I tried exporting another copy of the original mesh to make sure it wasn't a problem with my mesh, but those didn't work. So it's probably a button I've failed to click on somewhere or something u.u

You have to assign the texture to the mesh first:

In the Groups tab, use the Select button to select the mesh group.
In the Materials tab, click New in the bottom group of buttons, then click one of the wide buttons above there that's labelled <none>. Select a texture - usually your multiplier although it depends on what you're trying to do. Then click Assign in the bottom group of buttons.

Note that your solid model display window will have to be set to textured for it to show the texture. If necessary, right-click the window and select Textured. If you're using the multiplier the parts of the mesh corresponding to the transparent parts of the texture will disappear. (The parts where skin shows.)

Now when you open the texture coordinates window you should see the mesh.

Haha, of course it was something simple I managed to miss. I don't know how any of the creators have learnt to mesh as well as they do. It's so HARD, oh my lord.

Annnnndddd I'm DONE *wipes sweat off brow*. Thank you so so so much for all your help <333 I'm going to attempt a top to go with it, so it probably won't be long until I'm back in this forum :P

Looks very nice!