Hello ozboomer,
It is really difficult for me if not for everyone to provide an answer without seeing a minimal example of working code and what you are actually trying to achieve? I can see that you spend some time trying to put down all these analytical description but at least I need to see pieces of code and what you would expect to improve and how (sample of input and output as well).
Update: I found this question How do you use command line parameters? contains useful information such as module Getopt::Std and Getopt::Long for processing complex line arguments.
Looking forward to your update, BR.
Seeking for Perl wisdom...on the process of learning...not there...yet!
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