There are many good books about game/simulation design, although most are going to show their examples in other languages. I recommend you pick one up anyway - the concepts will be highly portable and it definitely looks like you need to do some research before starting this project!

On the other hand, maybe all you need is a hint. Here's one - most simulations use a global loop which increments every object once per pass and then updates the screen with the results. Something like:

   my $ticks = 0;
   while (1) {
      $_->update($ticks) foreach (@objects);
      $screen->draw(@objects);
      $ticks++;
   }
[download]

Each object is responsible for updating its state and exposes some kind of standard interface used by $screen to do the output (x, y, color, texture, etc). I don't know why you'd bother with XML and log files, but you could consider outputting them similar to re-drawing the screen.

-sam