Add use strict; use warnings; to the start of your program. Add declarations until it runs without warnings.

The scope of variables defined with my ends at the next closing brace. The scope of variables defined 'on the fly' (which is forbidden with use strict) ends at the end of the file.

> Will vars declared on the fly in the first loop be visible in the second loop?
Yes.

> Perl (with no main block)
It is good practice to put all your top-level code in a sub main($) { .. } and put main(\@_); at the end of your file; precisely because it separates the scope of variables local to the concepual or actual main from the purposefully global variables (which I assume you want to use to communicate between the loops).

What does "I'm having issues getting the script to run" mean? What is the exact error message?

In order to simply try your program, an input file would be needed, consider providing an example.

Also, your program is a bit long for debugreading, please try to reduce your problem by elimination.

Finally, please read How do I post a question effectively?