Can you not delete the empty folders from the iTunes folder, wherever it is stored? There must be a way to sort by folder size, in which case you can delete all the ones with 0 bytes.
It sounds to me like you've managed to mix up the old library with the new one. I think perhaps, if it was me, I'd delete the whole lot (making sure I had a backup first), then re-import the entire library from the old hard drive, thus creating a new library on the new drive.