Weight and alpha issues on a mesh

Hi. Not the best choice of an item to learn cc adapting for ts4.
1). If the mesh moved without clipping in another game, there is a way of rigging it properly in ts4. You could start by transferring weights from a skirt to s4studio_mesh_1 only. If the result won't be good, you'll have to edit the weights like this
2). Transfer weights and uvs with Nearest face interpolated;
3). You can watch this tutorial for more efficient uvs rearrangement
4). If you're making this for yourself and won't get distortions in-game, you can leave the package as is. If you plan on sharing it with other people, you should not start it from glasses. Glasses and pants function differently ( have different region map and slotraysinteractions). Normally we'd add a new meshgroup, which is a tedious process
5). The transparency issue you're seeing is called alpha sorting. The game does not know which part of the skirt comes first, what to render first. To fix it, you'd need to separate the front, then the back, then join them again. It may not work out fully at first

It'd be best to postpone finishing this garment because it has all 3 the most troublesome things in cc adapting for ts4.

2). Using nearest face interpolated for uv transfer results in better uv_1 so that the mesh morphs better. That was not meant to remove clipping, that is purely weight editing;
4). That is also not the best thing to do. The bg pants are split into multiple meshgroups for each part to have different Regiontype. They are affected by different bones and have different slots in slotrayinteractions. So when you replace any of these parts with your s4studio_mesh_1 that is affected by different bones and is not meant to be hidden upon interaction with tall boots, unwanted things can happen.
5). Are you merging them into one in milkshape?

Yep, did some testing, can't layer it.
- make geometry one-sided with Remove doubles, then Recalculate outside;
- then take Knife tool and cut out the black, as you do this, mark the new edges as Sharp, will be easier to delete;
- once done, select the face in the unwanted area, Ctrl L, choose Sharp, Delete - Faces;