If you want to speed up your code, you need to find out what's taking up the most time. The way to do that is to use a profiler, probably on a reduced-size run. You can try Devel::DProf, Devel::Profile or perhaps Devel::SmallProf.

Once you know where the time is being spent you can work on finding a faster way to do it. You could post again with a more specific question, revealing perhaps what's actually done in the middle of your innermost loop.

-sam