Okay- I just realized a better phrasing....
What I am having an issue with is getting the hashes to match up with a file. You can see that in the code I have sofar it opens up the config and runs a hash against all of the lines in the file, then it stores the hashes into a file. The problem lies here for me:

if ($NEW-HASH-RUN <> $OLD-HASH-RUN) {
print "The system file: $file is different.";
}