If you are handling the CSV files in Perl, you might also want to do the database interaction with your Perl scripts to keep it all together. It is possible to query/manipulate an MSAccess database from Perl using the DBI module. See DBD::ODBC
In this particular instance, I'm looking to get rid of any reliance on MsAccess. It's purely accidental that I use Access now; it just happened that I could write the app within Access as a module as it was available at work so I could use their time to write it (and leave more time for beer at home).
Database connectivity isn't a requirement for this, I want it to stand alone though I can see that it could be useful for future projects.
If your data collection is large (for any value of large), DBD::CSV might grow (very) slow. For relatively small dtasets, DBD::CSV gives you instant relief: combining CSV files and selecting from one based on contents of others gets dead easy. When the dataset grows, and you still do not need a full relational dtabase like PostgreSQL or MariaDB, DBD::SQLite might be the interface of choice.