One thing. I would change this:

while(<IN2>) {
    chomp;
    print "$_ is a new site\n" 
      if not defined($newsite1{$_});
  } # while
[download]

to this:

while(<IN2>) {
    chomp;
    print "$_ is a new site\n" unless exists $newsite1{$_};
  } # while
[download]

Checking for the existence of a key is quicker than looking up the value of a hash element.