i coppied my windows XP game into a Windows 7 machine for awhile.
all i did was copy: meshes, textures, sounds, music, icons (yeh. all the vanilla folders, jst fill with mods)
then every mod added esp\esm
and then my saves and the ini
i didn't copy the original esm's. or the whole folder, i just installed a fresh morrowind, and copied everything over, like installing a GIANT mod.
might work for you?