Thanks for the suggestions! Here's what I found...

I already changed the loops to use foreach; that seemed to be a little faster, and a lot more readable, so all benchmarks already have that in it. Here's what the numbers looked like before the other two changes:

Total Elapsed Time = 43.18577 Seconds
  User+System Time = 42.69577 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 48.8   20.83 20.710 130000   0.0002 0.0002  FTS::printto

Changing if(!defined($sec)) to unless($sec) seemed to slow printto down just a hair. This could just be measurement error; for some reason apparently other parts of the code sped up with this change, which again points to measurement error...

Total Elapsed Time = 41.62356 Seconds
  User+System Time = 41.09356 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 51.3   21.09 20.905 130000   0.0002 0.0002  FTS::printto

Changing print $fh to $fh->print seemed to slow things down significantly. The IO::Handle::print changes who the print calls get charged to, so the ExclSec for printto goes down, but it's made up for by all the calls to IO::Handle::print, and the CumulS and overall time go way up...

Total Elapsed Time = 51.91479 Seconds
  User+System Time = 51.32479 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 41.5   21.31 18.510 281000   0.0000 0.0000  IO::Handle::print
 38.9   19.97 35.589 130000   0.0002 0.0003  FTS::printto