I'd firstly go through the original files, trying to make sure they use a consistant naming convention, which will help in the importing.
(You can then adjust the 'adding books' regex in preferences and 'use filename for metadata')
series series# - title - author
Or
author - series series# - title
Then when importing (in batches), they'll be fairly organised, you can then use the plugins to get the other metadata and tags etc - upgrade covers.
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