You have your file-opening code inside the loop through each line. It should be moved outside, so the file is only opened once instead of once for every line (and overwritten each time), and also would be better written as:

open my $OUTPUT, '>', $outputfile or die "File open fail: $!\n";
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See open.

As far as your data foramtting question, you probably should use a module for reading your Windows file format, maybe Win32::OLE? (disclaimer: I haven't programmed with Windows for years; search CPAN and you'll almost certainly find what you need if that's not it.)

Hope this helps!