You will get better answers if you show us a "before and after" of the input and output files. Wordy descriptions are likely not to be accurate nor accurately understood.

Note that PerlMonks isn't a code writing service. We would much rather help you improve your own code and learn in the process than simply write the code for you. Perhaps you could do enough work to at least sketch out a solution yourself? Note that CPAN is your friend for tasks like this.