I just recently wrote a script that was doing the same thing
with a much smaller sized file yet it didn't run as fast I thought
it should.

Turns out I had a bug in the script.

Here's the buggy script:

...
my $tabCount = 0;
my $line     = "";

while(<>) {
     ...
     $tabCount += $#tabs+1;
     $line .= $_;
     if ( $tabCount == ENOUGH_TABS ) {
         print "$line\n";
         $tabCount = 0;
     }
}
[download]

The bug is that I was not doing
$line = "";
when I was doing
$tabCount = 0;
thus printing a larger $line
everytime and slowing things way down.
I dunno but you might wanna make sure you don't
have a bone head bugs like mine :)
Good luck!