It seems to me that this project can be split into three parts: Collect the data, store the data and then display the data.

You have chosen to store the data in mySQL, which leaves the other two tasks. Perl could easily handle collecting the data and passing it to the database, java may be better at displaying the data. As long as the database remains the same the two parts could be dealt with seperately. That said if your main display method will be over the web then Perl would be a good bet.

Prototype in perl, and unless there is a compelling reason to change, keep it in perl.