This code could be considerably shortened, and made easier to read, as well as faster, if you re-do it in idomatic perl.

To get you started in that direction:

* Use meaningful variable names
* Error check each file open by adding open(...) or die "Could not open <filename>:$!";
* Do not repeatedly loop over the same arrays
    Do all necessary processing in a single loop over the array.
* Use appropriate data structures: Use a hash for word lookups .
* Use subroutines for repeated code.

In addition, for questions to PM, be clear on what the inputs, and expected outputs look like. Also, a clear problem statement, and a polite request would probably induce someone to write it for you, since we have seen that you have put effort into doing this.