I violate the rules regarding global variable, strict and warnings.

Making it strict and warnings compliant was not very difficult and could be carried out in a quite mechanical way:

• strict was satified after declaring 6 more sub-specific variables with my.
• warnings were issued for using non-existant array/hash values. I silenced these by looking what kind of data is expected and making an appropriate || fallback, e.g. line 278 became:
  ($nl, $nd) = ( scalar(@{ ($tmp_across{$cur}||=[])->{locs} ||=[] }), scalar(@{ ($tmp_across{$cur}||=[])->{nums} ||=[] }) );
  this way

All in all not very demanding and nothing which should have caused much headache had your script been started with use strict; use warnings; as the first keystrokes right from the beginning of creating it.

As for the global variables... at least they already were cleanly declared, YMMV.