First, its a good idea to seek advice and review. I regularly write stuff that I think is good until one of my colleagues points out that he would have done it better/ faster/ in less code by doing it another way.... :-)
Second, the main mistake you made is that you didn't ask yourself what tasks in the above script could be done by standard PERL libraries instead of lovingly hand crafting every aspect. There are lots of text parsing libraries, which if used, would have the benefit of substantially simplifying your code.
In future, spend a few minutes before commencing any programming task, asking yourself what someone is likely to have done before, and what you can borrow from others to simplify your task and to make your code more understandable and maintainable.
A quick browse of CPAN or PerlMonks before you program will often save someone dissecting where you went wrong afterwards. That said, good luck in the future! :-)
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