I'm short on time, so I can't answer all of your questions, but let me take address a few items, quickly.
1) I would probably convert everything to ePub, but there is probably no reason to delete other versions (unless you're short on space).
2) As to cleaning metadata, I'd suggest adding a custom column (I call mine "MetaFix"). The column should be a three-way Yes/No column. When you fix metadata for a book, change that column to Yes. This way, you can do searches for books that have metadata that needs to be cleaned (or have Calibre temporarily hide books that have already been cleaned). I also tend to sort by author and then title (or date) when cleaning metadata so that I can work with similar books in sequence.
Hope those ideas help a bit. Good luck.
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