Today I discovered that how AA2 did lipstick is it kept a separate mesh of just the lip area, whose vertices were otherwise identical to the face mesh, over which a transparent lip-color texture was laid, and then the whole thing was superimposed over the face at the exact right point so that nobody would be able to tell there was a redundant mesh there.
Of course, when you rip all the meshes out of memory, and all the textures, and then cram them into blender with a third party import addon, then export them with yet another 3rd party addon to change the model meshes into PMX format so the MMD editor can read and manipulate them, some things get lost along the way. So, in order to save Shego's lipstick, I had to re-find which mesh was the lipstick mesh (it was #254, incidentally) using Open3Mod, then download and install paint.net because it has native dds support (for the texture files) since photoshop was being a butt about loading DDSes and the plugins I found weren't helping...
So then I took the mesh back into blender, and saved it as a PMX with no texture, loaded the lipstick texture into paint.net and re-saved it as a png to maintain its transparency, then loaded the lip pmx into PMXe and assigned it the lipstick.png texture.
And that was the easy part.
Then I had to EVER SO METICULOUSLY move the lip mesh into place over the face mesh's lips in such a way there would not be any visible overlap.
See all those little green dots? Those are vertices. See the orange dots? Those are the vertices I'm trying to perfectly overlay on them. It was pretty difficult.
But I think I managed.
Incidentally, Shego has about as many separate meshes in her hair as Amy had in her entire body, give or take 10% or so. And I intend to make it physics enabled! THAT will be fun.