That's the order you are printing in, isn't it?

       if ($mc_value) {
        print "\t" . ' ' x length $p_value;}
        $mc_value=$line;
        print "\t$mc_value";
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Yes, or you can select OUT; before your first print statement. That selects OUT as the default filehandle for output.

Another suggestion. You have instances like this:

     } elsif ($line=~/\bProcessing\s/) {
            $line=~s/\bProcessing\s\d+\.tx\.\d+: //;
            $u_value = $line;
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Which could be simplified:

     } elsif ($line=~s/\bProcessing\s\d+\.tx\.\d+: //){
            $u_value = $line;
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And you could simplify throughout with $_ instead of $line, but that's a matter of preference.