I agree with reneeb that you need the extra '/' in the global substitution. However, there's no reason for the backslashes in the regular expressions.  Neither quotes (") nor commas (,) are regular-expression metacharacters, so just write them like this:

    while($_line1 =~ /"/) {
       ...
    $_extraLine1 =~ s/,//g;
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Is there some reason you're not using "use strict" and "use warnings"?  They're very useful, and would point out the locations where you've neglected to create lexically-scoped variables with my.  You may also want to rethink the use of leading '_' in your variable names, which typically have the connotation of being a program-internal variable.  And finally, do you really want the clutter of comments like:

    }# End the check to see if contained another quote.
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and

    }# End  while statement
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in the code?   It's pretty easy to see where the opening '{' for each of them are; all the more so if you indent prudently and don't add unhelpful comments to the mix.