Here is my process.
1) Create an MH character and export to Blender.
2) Import character into blender.
3) Fashion some low poly clothes including just the basics, boots, pants, and shirt.
4) Add automatic weights to all the clothing and fix some of the weighting with weight paint. Posing looks great.
5) Delete the MH verteses that are under the clothing since they are no longer needed to reduce poly count.
6) Go to the materials of the properties page and select "Save this datablock even if it has no users" for each of the materials. (Not even sure if this is necessary, but I saw it in a tutorial once.)
7) Select my player mesh, and all clothing, then export the selected items to FBX file.
8) Add the FBX file as an asset and move the MH textures into a texture folder of unity.
9) Map the MH texture file to all of the necessary shader properties of the character.
Everything so far as I know should be correct. But I get this as a result.