Umm,

Have you tried turning on warnings and rerunning it - you don't give any diagnostic messages, which would make your life considerably easier. It might well be worth use strict; ing too, given the size of the script.

My guess is that you've incorrectly escaped/matched a quote somewhere and blown though some lines...

Elgon

PS - You also may wish to consider using transobliteration instead of substitution as it is quicker.