Yes, this is a very common problem when doing system conversions. There's no real magic way to do it: once you have a record in memory, you have to populate several tables with it, which involves looking up the ID and inserting the row. With SQL Server, you can use stored procedures to handle the multiple lookups and inserts.

If your database has RI enabled, you have to be careful what order you populate things in. If the entire flat file will fit into memory, you can make sure all your reference data is correct before you start inserting the main data. It's a small simplification, but it can help.

In other words, use Perl to break up the flat file, then use SQL to populate the target tables. Since you're only populating three tables, it doesn't sound too complicated. With SS7, you can use DTS to control the process, although a single pass through the Perl script may be sufficient.

With something this size, you have to balance the effort of customizing a package versus writing custom code. It may just be a wash.

If you run into trouble, my consulting rates are very reasonable. ;-)