[dickloraine]

I use just one calibre instance with multiple libraries.

I don't read mangas, so I don't know. Comicrack and Comictagger use comic vine as their database. If the manga are there, it should work. Comicrack and Comictagger do the exact same thing, so if comicrack doesn't work, comictagger wouldn't work either.
I don't use comicrack anymore, but as far as I know, it has scripts. Maybe there are scripts specific for manga metadata for it?

My plugin doesn't download any metadata. It just imports existing metadata in cbz/cbr files into calibre. I just know/like calibre better than comicrack and my plugin allows the reading/writing of comicrack metadada embedded in comics.