I think you should be able to do this with MC, provided the art is stored in folders that properly identify Artist and Album (or the art files are tagged)
I'll have to test, but the basic idea is:
- import the Y:\coverart files
- tag cover art's Artist and Album using portions of the source file path
- Copy using Rename, Move, & Copy, pulling from the just-assigned Artist and Album tags
- Update MC's cover art location, selecting Audio mode: In the same folder as the file (as Folder.jpg)