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My first recommendation is to come up with a way to identify which books you've already "cleaned," i.e. fixed the metadata. That way, you can measure your progress and know when you're done. I use a custom Yes/No field. Other people use an intake library where they clean up the book then transfer it to their main library.
One of the first decisions you should make is whether to make the Tags column hierarchical. Non-hierarchical tags would be things like "Fantasy" or "Historical Fiction". Hierarchical tags would be things like "Fiction.Fantasy" or "Fiction.Historical". You can set up Calibre to treat these as subcategories, as many levels deep as you want.
One thing to keep in mind is that tags only exist if they are used in at least one book. You could create a dummy book with all the tags you want to use, so that they exist before you start applying them.
You can rename field values in the tag browser. It's okay to rename a field value to something that already exists; that will "merge" the old value with the new. This can be a huge help in normalizing your data.
You can download metadata, but sometimes the results are inconsistent or illogical. Treat downloaded metadata as merely suggestions. Always do a manual confirmation afterward.
These are just a few suggestions I thought of. I hope they help.
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