perltidy can beuatify your code in a blink but no one but you can put more effort when choosing variable names. I tell this because occured to me, and passed some weeks, i never could re-understand my own code. Even more important if someone else looks at your code: a well choosed name can do the differnce and few keystroke more are worth in the distance.

Anyway if you just want intersection of two lists is faq, see How can I find the union/difference/intersection of two arrays?. Using exists on a hash list of keys can be usefull.

If i've understood your question you can try something like

# untested

while (<$first_fh>){
      chomp;
      my %infirst;
      # every word become a key of temporary hash
      map{$infirst{$_}++} split ' ',$_;

      my $ref_line = <$second_fh>;
      chomp $ref_line;
      print grep {exists $infirst{$_}} split ' ',$ref_line;

      die "$file_one exhausted!" if eof($first_fh);
      die "$file_two exhausted!" if eof($second_fh);
}
[download]

For large files be awere to never evaluate <$fh> il list context: see recent Re: How to read in large files

L*