First off, why are you doing two sorts? Sorts are pretty damn expensive (or so I'm told). Especially in this case, I would imagine, since hash lookups on anagrams (act, atc, cat, cta, tat, tca) are particularly slow. Being timestamps they are restricted to a 10 character set, and most likely be all of the same length, thusly ensuring that a portion of a decent sized will be anagrams.

($j, $l) = (sort keys %master)[0,-1];
[download]

Second

#Might go with a C-style for-loop here.
while($j <= $l){
 for my $elem (qw(CCMT ...)){
  $out .= "," . ($master{$j}{$elem} || '0');
 }
 $j+=60;
}
[download]

--
perl -pe "s/\b;([mnst])/'\1/mg"