I frankensteined four meshes together into a coherent mesh (an af dress), with vertices snapped together and data merged, bone tool'd, normals aligned, vertices auto numbered, comments copied, uv map fixed, welded, and shifted, lesser LODs made, etc.

I figured I'd worry about the morphs later, but am beginning to think I did everything in the wrong order and should have worried about the morphs in the beginning (as per morph mangle's notes.) I cannot import the extracted morphs from my base mesh onto my new mesh because the vertex count is now off.

Is there no way to salvage my mesh?

i wouldn't gamble on also frankensteining the morphs from those 4 meshes, it is asking for trouble.
So you might aswell continue and duplicate your custom mesh 4 times and shape each into a morph.

If you still want those original morphs and try i suggest you import the original mesh+morphs, then import your custom mesh.

What you need to do is keep the mesh parts separate in order to get the morphs. What you should do is this:
-Import your base meshes into milkshape.
-make your changes.
-use those with the UNCHANGED morphs in Morph Match Maker.
-then fix those in milkshape, MMM isn't perfect but it does the majority of the work for you. I'd suggest doing one morph at a time because your going to end up with a lot of groups using four meshes. I have a hard of enough time using three.
-once all the morphs and the bases are the way you need them to be, then you can renumber, regroup and fix the comments.
I have done this numerous times with great results but every once in a while when I've gone to renumber it's thrown an error at me, could have been my fault, could not have been, who knows.

Just so I never make this mistake again (because I am sitting on about six "finished" meshes right now and I feel exceedingly distraught about having wasted my time): Keep everything separate until after I've done the morphs?

I assume I am unable to delete any vertices from any of the meshes I am working with until after I've done the morphs?

If you want to use morph match maker, yes. I would think that is easier than doing it yourself, no?

I'm not sure I understand your second question. Your morphs must have the same exact number of verts as your base, otherwise they won't work. With MMM you need the altered base mesh and the unaltered morphs, so maybe the answer is no. You can remove verts from the base before the moprhs.

Thanks for clarifying, and yeah, you understood my second question perfectly.

I shall never make the same mistake again, at least.