Your latest question (--) seems to me to suggest that you ignored or didn't understand ikegami's earlier explanation that text-wrapping MEANS inserting a <CR> at the end of the (wrapped) line... and the observation that Text::Wrap breaks on word boundaries.

Then, your comment,

012: # strip out all Carriage Returns
013: #
014: # Process the file by replacing each tilde (~) with a carriage return / line feed and
015: # save the file in the correct file format.

matches neither what you say you want to do, nor what you are doing. There's no mechanism in your code to remove "carriage returns" ... and you can't very well replace each tilde with a "carriage return" and retain the tildes.

What's more, the output I see appears to retain the tildes.

So perhaps you should clarify your question (preferably, after clearing up your understanding of what text-wrapping IS and what Text::Wrap DOES (for which, perldoc Text::Wrap should help.)