Some random thoughts:

• This isn't a Perl-specific question - it's a generic question about massaging data before inserting to a datastore.
• If speed is an issue, then the bulk-loader is the right way to do it.
• Determining uniqueness is a problem for a hash. Or, in your case, a hash-of-hashes-of-hashes (HoHoH)
• Auto-incrementing a PK is a matter of inserting NULL. Read the documentation for your bulk-loader.
• In fact, read the documentation for all the pieces you're working with. Most of the questions you have answered in the FAQ for each.

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