My question is this: is there a way of breaking it into smaller chunks for files instead of having everything in one large file? I have done this in other languages and it makes things much more readable.
If what you mean is: "a way of breaking it into smaller chunks for files automatically?", yes, you can split your code using a custom record separator (like "\n\nsub "). See the special variables $/ and $\ in: perldoc perlvar.
Using this you can pick up chunks of code containing perl objects and print each different function in your code to a different file (function1, function2... use a counter) to be examinated. You will need a little post-processing for fine-tuning probably