I thought I was ready to tie up the loose ends on this project. Pop out lod2 and 3, package it, and move on. When I opened it in game though, there are some really ugly dark spots scattered over the shorts. They don't show in TSRW or Milkshape. The normals look horrible in CTU, but they're different than what appears in the game. I've tried selecting the area and aligning the normals from the drop-down menu, but it has no effect. From where the problems are, it looks like they've been with the shorts since I first duplicated and mirrored the sides. I had a similar area show up on the open front shirt I did, but the problem only showed up in CTU. It was fine in game.
To allow for larger textures, I overlapped the shorts on the UV map. L and R front are overlapped, and so are the R and L backs -- could that be causing the problem? The belt is also overlapped though, and it looks fine. It's made of 4 pieces all stacked 1 on top of the other.
I feel like I don't have much control of the normals with Milkshape. These are some pretty noticeable problems, but noting I do seems to have any effect on them at all. Any suggestions?

Overlapping the UV will definitely cause an oddly shadowed or even stripy appearance in CAS which usually does not appear in-game. How do the shorts look in-game? As for the top, if you didn't overlap the UV there something else must be causing it.

Looks to me those are unmapped faces?

The pics I provided are from CAS. I didn't enter the world -- when I saw the god awful textures I quit the game. The top is also overlapped. I was trying to get nice, crisp textures on all the different pieces and thought by overlapping and making the textures larger, I could get those results. Since I made this post I started messing around with the geoms I made the mesh from, and am re-working the main body of the pants AGAIN. I think I can reduce the poly count there by about 60%! Hopefully the overlapped texture will look better in-game. I'll take a look at it as soon as I finish up the main part of the pants. I can't imagine how any faces could have gone unmapped, but I've worked this mesh so many times anything is possible. If the problem is still there in the game, I'll use the remap option and start from scratch. Thanks!

A test by applying a pattern to the mesh in Milkshape should give similar results(if those are unmapped)

The odd looking triangles disappear in-game. Like Cmar said, they must show up in CAS due to the overlap. The normals on the bottoms are a little wonky still, but I can live with that. The textures are still a little too bright, but that's to be expected since I haven't really worked on them much. Reducing the poly count was a bad idea. The mesh lost its smoothness and looked really chunky. I'm going to finish the textures, make the lower lod's, and move on to something new. I'm really tired of looking at these blasted shorts. Thanks for the help everyone!

did you update the normalmap on all 3 lods already?

I see you've made huge progress with this and it looks fantastic.
I tried making a skirt for the GND and it looked horrible.

Thanks Julie -- I should be posting this on BAS later today. I'll try posting it here, but MTS doesn't like the high poly count, and I think they may have a problem with the detailed breast cups. I did try to make the full body nude post on the MTS adult site, but every time I try to open the upload manager I get redirected back to the family site?!? It could very well be my browser -- there are a few websites I can't seem to open at all, one of them being the Sims 3 store.
Once I updated all of the textures including the normal, specular, and alpha maps, everything looked MUCH better in-game but they do still look odd in CAS. There's a very strange problem popping up though. Once all the textures are loaded, I can go into the texture editor and change the COLORS on all 4 mask areas, but I can't change the MATERIALS! TSRW crashes and CTU won't show any changes. I'm just attributing this to the huge amount of overlap I used on this mesh and will use the base texture for a single custom recolor. The materials can be changed in-game, so anyone that installs the package will be able to make it look however they want. I think I'm going to attempt a new top next. The breasts are really large though, and the few things I've tried haven't looked very good. Maybe with some real effort ---

What I do is put Milkshape into wire frame mode and move the pixels to fit the breast.
Long process but it does work

Downloaded it - can't wait to play with it in game.