At first sight, this looks like a mess, but it's actually not so bad.
The good part: you have divided the work into manageable pieces (subs). The bad part: an enormous amount of global vars make it hard to follow.
To rewrite, I would start by building up an array of hashes. The array represents the lines from the csv-file, and the hashes is the data on each line. Iterating over the csv file you decide if the current line is to be included or treated special. A simple rewrite of the template, and feed the AoH to it. Done.
cheers
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