Reading the comments and suggestions of others, and your response to them, it looks to me as though you've bitten off slightly more than you can chew for a first project. I suggest that, since you've broken down your project into six major goals, you should consider each of those goals as a project in itself. Work on a single item from your list of goals, and when you are happy that it does what you need/want, move on to the next item. When that one's done, maybe play with integrating the two so they work together. The key is to start off simple. The program can build in complexity as you become more comfortable and competent (in Perl), having solved each problem.

It took me a long time to learn this lesson! And I (stubbornly) had to learn it for each discipline I tackled, be it mathematics, physics, or computer programming.