Judging from the fit of the neck (in the first set of pics), I would say that your modified mesh isn't even loaded - or you haven't imported your changes properly.  The screenshots you have provided look exactly like the unmodified adult mesh.

One way you can verify if your mesh edits are taking is to grab one of the neck vertices and do something ridiculous with it (create a giant spike).  If it shows up in the SimPE preview window and Body Shop you know you are loading your exported mesh correctly.  If not, you need to revisit the above steps and make sure you're re-importing the modified file you exported from Milkshape.  Also, did you remember to scale your model by 0.94 before adjusting the verticies?

Here's a screen shot of the earlier formal I posted:

First things first...get rid of those ridiculous blue lines so you can see what you're doing  File | Preferences | Misc and set Joint Size to something MUCH smaller - like 0.005 (you can tailor to personal preference).  Then on the tool palette, select the Groups tab.  Hide all groups except "body".  Then go to the Joints tab.  And select the neck joint.  This will auto-select all the neck vertices assigned to that bone.  Then go to the Model tab, enable "Move" mode, then gently click and drag in either of the top 2 projection views to lower the verts.  You can also use the arrow keys to "nudge" them into position.

J

Spend some time here:

http://forums.modthesims2.com/forumdisplay.php?f=114

The Body Chop plug-in is here:

http://forums.modthesims2.com/showthread.php?t=50219

Milkshape can be found here:

http://www.swissquake.ch/chumbalum-soft

Sorry, my cup already overfloweth as it is

Well, if you're asking me if you can share a mesh and use it for multiple pieces of clothing - yes, you can.  But you should understand that there are different clothing styles that have completely different geometry.  A sundress and a pant suit have very little geometric commonality whatsoever, so you would need to make edits to both separately.  However, once you did this, you could re-use that sundress mesh to make a dozen different sun-dress styles by altering the textures, alpha, and normal maps.  You can create some very different looks just through texture alone.  With normal maps you can "fake" geometry.  For instance, if you look at the sweat pants, you'll notice that the bow string is textured - not modelled...there's no geometry there - it's just a trick of light and shadow.  The wrinkles and pleats in the above dress are also "fakery".

Sadly, there is no one mesh you can change that will work for everything.  When you change a sims clothing, while the textures are overlaid on top of one another, you are replacing the entire geometry of the body.  Just gotta buckle down, and get your hands grubby

J

The problem arises from the fact that adult meshes are 6% larger than the teen meshes.  The length of the neck in the adult is also longer than the teen, so the neck from an adult mesh will protrude into the mesh that makes up the teen head.  I am dealing with this very problem as we speak with InTeen since some of the outfits are derived from adult meshes.  What you need to do is download Milkeshape, export the GMDC from SimPE, use Wes_H body chop plugin to import the GMDC mesh into body chop, scale the entire mesh by 94%, then adjust the neck verticies (the latter will take some trial and error).  You'll then re-export the GMDC using Body Chop, finally importing the new mesh back into the package file using SimPE.  It's important that you use the REPLACE (right click and then Replace) functionality and not the GMDC Import/Export - as it does not deal with bones or body morphs (fat/pregnant) correctly. The idea is to get the lower neck vertices of the head to line up with the upper neck vertices of the body.  When you do this, the surface normals for those polys will align correctly and the light will fall evenly across that seam.

In short:

1. Extract the adult GMDC mesh as .5gd file using SimPE
2. Open Milkshape and choose Import > Body Chop and open the .5gd file you created in Step #1
3. Use the scaling utility (in Milkshape) under Tools to scale the mesh to 94% of its original size
4. Lower the ten neck verticies (and move them back slightly).  
5. Use Export > Body Chop which will create a new .simpe file
6. Go back to SimPE, right click on the original GMDC mesh, and select Replace and open the file you exported in Step #5
7. Save
8. Inspect your changes; lather; rinse; repeat as necessary

Wow.  Those are some impressive shots.  Neat pad!

I think SimReal house is in need of a skinny-dipping pond if it ever gets ressurected.

Wow, Toni.  Those pix are incredible.  That totally rocks.