If I understand you correctly you need to:

• Do MySQL db inserts which will require the DBI module
• After you've determined the format of the file (Perl's regular expressions should help provide an indication of the file format unless it's just a different sort order within CSV files)
• and parsed the file using the appropriate parser eg. XML::Simple, Text::CSV
• As to the other spec elements, buy a copy of Perl Best Practices and apply its wisdom.

Or to put it another way, that is not a question, it's a job spec - write some code, tell us what's going wrong if you are having problems otherwise try offering to pay someone to resolve the issue.