At a cursory inspection it looks like this module is something that I'd use instead of Regular expressions. (Unless you can call a Perl Function from within a Regex. Can you do that? (OMG according to http://www.perlmonks.org/?node_id=832028 you can do just that. My head is going to explode!)). I'm not ready to give up on Regex's yet. I can decompose

\(bunch_of_ugly_subscripts\)

into

\(uglysub,)*uglysub\)

and then maybe I'd use variable substitition in the regex and create a separate regex variable that's an alternation for the different kinds of ugly subscripts:

$UG = 'notsougly|uglywith"|uglywith\'|...';

This would be updatable as I encounter different outrageous subscripts. Maybe I'd use calls to the Text::Balanced module functions in here?