One helpful hint: you almost never want to read a file in a "for" loop as you have it. You are reading the entire file into memory. If you don't care about reading the whole thing into memory, then you may as well do:

my @file1 = chomp( <IN1> );
my @file2 = chomp( <IN2> );
my $last = (@file1 > @file2) ? $#file1 : $#file2;
for my $line (0..$last) {
  print "$file1[$line] $file2[$line]\n";
}
[download]

If you don't want to read the entire contents into memory, then you'll need to eliminate the inner loop. Something like:

{
  my $line1 = <IN1>;
  my $line2 = <IN2>;
  last unless $line1 or $line2;
  chomp for $line1, $line2;
  print "$line1 $line2\n";
  redo;
}
[download]