Are you using Perl CGI or a framework such as Dancer / Dancer2 / Mojoliciious / Catalyst? I have experience with CGI and Dancer2. How many collections does your MongoDB have - and can you show me the schema?
I would be able to give you a more accurate bid after seeing the existing Perl script(s). It is very difficult to give an accurate bid otherwise. So this bid is PROVISIONAL until I have more details. The work might only take a few hours, but - without more information - it is impossible to tell.
If server access is required, I prefer using SSH - but I can use cPanel if necessary.
My DB experience is mainly with SQL databases (MySQL, PostgreSQL) but I can use MongoDB also.
I am based in Ireland.