G'day immamanatee,

Welcome to the monastery.

You're reading your data an inordinate amount of times:

• Read all input into $text using slurp mode ($/ = undef).
• Read all data to generate @url_list.
• Read all data to remove URL lines.
• Read all remaining lines in an outer loop.
• Read each line in an inner loop to generate link numbers.
• Read the entire @url_list in every pass through the inner loop.

As you're dealing with paragraphs, consider reading your input as paragraphs and processing it just once:

• Read all input into an array using paragraph mode ($/ = '').
• Create a hash, mapping link number to URL, using just the last paragraph of text.
• Loop through all but the last paragraph, printing each paragraph and any associated footnotes.

Here's an example using your data:

#!/usr/bin/env perl -l

use strict;
use warnings;

my @data = do { local $/ = ''; <DATA> };
my %urls = map { /^\[(\d+)/ => $_  } split /^/ => $data[-1];
print $data[$_], @urls{$data[$_] =~ /\[.*?\]\[(\d+)\]/g} for 0 .. $#da
+ta - 1;

__DATA__
This is a an example of [Markdown][1] footer links. I'm trying to use 
+[Perl][2] to organize them more coherently.

But I'm getting too many newlines and I'm hoping the [PerlMonks][3] ca
+n help.

[1]: https://daringfireball.net/projects/markdown/
[2]: http://www.perl.org/
[3]: http://www.perlmonks.org/
[download]

Output:

This is a an example of [Markdown][1] footer links. I'm trying to use 
+[Perl][2] to organize them more coherently.

[1]: https://daringfireball.net/projects/markdown/
[2]: http://www.perl.org/

But I'm getting too many newlines and I'm hoping the [PerlMonks][3] ca
+n help.

[3]: http://www.perlmonks.org/
[download]