Having integrated comments from fellow monks I would suggest four additional changes:

1. In the second file, compute and store the length of the sequence alongside the sequence. Ignore headers.
2. When picking a random sequence first filter on the required length. This might slow things down if sequences in file 1 are much shorter than in file 2 but give it a try.
3. Subtract the desired size from the length before determining the starting point of the sequence.
4. Print the sequences into the output file directly instead of first storing them in an array. This saves another array.

I have no time now to test my code, so apologies for any mistakes...

use strict;
use warnings;

my $start_time = time;
my $input1 = shift @ARGV;
my $input2 = shift @ARGV;

my %dstrbtn_hash;
open(IN1, '<', $input1) or die "Can't read source file $input1 : $!\n"
+;
while(<IN1>){
    chomp;
    $dstrbtn_hash{ length($_) }++ unless />/;
}
close IN1;

open(IN2, '<', $input2) or die "Can't read source file $input2 : $!\n"
+;
my @source;
while(<IN2>){
    # ignore header
    my $seq = <IN2>;
    chomp $seq;
    my $len = length( $seq );
    push @source, [ $seq, $len ]; # keep length alongside with header
}
close IN2;

my $filename = $input1.$input2."_extracted_seqs.fasta";
open (OUT, '>', $filename) or die "Can't write to file $filename : $!\
+n";

my $header_count = 1;
while( my ($key, $freq) = each %dstrbtn_hash) {
    my $size = $key - 3; 
    for my $iteration (1..$freq) {
        my $temp_source_seq;
        my @cand;
      EXTRACT: 
        {
            @cand = map { $_->[0] } grep { $_->[1] >= $size } @source;
+ # filter sequences long enough
            die "No long enough sequence found in $input2\n" unless @c
+and;
            my $chosen=int(rand(@cand));
            $temp_source_seq = $cand[$chosen];
        }
      START:
        {
            my $temp_source_seq_len = length ($temp_source_seq);
            my $random_start_coord = int(rand($temp_source_seq_len-$si
+ze)); # substract $size to avoid loop
            my $extracted_seq = substr($temp_source_seq, $random_start
+_coord, $size);
            print OUT ">".$header_count."extracted_seq", "\n";
            print OUT $extracted_seq, "\n";
            $header_count++;
        }
    }
}

close OUT;
my $end_time = time;
my $duration = ($end_time - $start_time)/60;
print "Thank you for your patience, this Perl script operation has com
+pleted, it took $duration minutes, good bye!", " \n";
[download]

UPDATE: Couple of changes pointed out by karlgoethebier. Thanks!

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