Your analysis of the problem is quite accurate. If you do those steps, one at a time, you get what you want. Keep in mind that hashes can't be sorted, just their keys and/or values.

I would like to sort Hash “A” (key) in descending order

my @sorted_scores = sort { $b <=> $a } keys %HashA;
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and then align the (value) Hash “A” with Hash “B” (key).

my @sorted_words = map { $HashA{$_} } @sorted_scores;
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Then use that sort, to align Hash “C” so that the key value pairs of "C" can be printed out in the same order as the sorted “A” Hash.

my @sorted_line_nums = map { $HashB{$_} } @sorted_words;
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And the print:

print($HashC{$_}, "\n");
   foreach @sorted_line_nums;
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All together now:

print("$_\n");
   foreach map { $HashC{$HashB{$HashA{$_}}} }
           sort { $b <=> $a }
           keys %HashA;
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I'm curious as to how you handle two lines having the same score, if the score is the key.

Thanks very much for the help.
Could you explain further how to use the sorted hash "A" to align the second hash "B"

There's no such thing as a sorted hash(*), and I don't know what kind of terminology "align" is. You're confusing yourself by trying to be technical. Your data does NOT consist of unsorted hashes, sorted hashes and alignments; your data consists of scores, keywords, line numbers, text and the relationships between them.

Your question is then "Could you explain further how to get the keywords for a list of (sorted) scores?" I used:

my @sorted_words = map { $HashA{$_} } @sorted_scores;
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I could also have used:

my @sorted_words;
foreach (@sorted_scores) {
   push(@sorted_words, $HashA{$_};
}
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%HashA defines the relationship between scores and keywords. To get a list of keywords for a list of scores, simply loop over all the scores and use %HashA to find the corresponding keywords.

* - Well, it's possible using tie, but that's neither needed nor relevant here.

To be honest, that doesn't seem too bad - what have you tried?

Hint: you'll want intermediate arrays to keep track of the sort order.