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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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.

I don't get why you didn't use a hash slice.

my @sorted_words = @HashA{@sorted_scores};
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   push(@sorted_words = $HashA{$_};
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That is sooo wrong, I can't believe you wrote that.

   push @sorted_words, $HashA{$_};
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Goind points. The second was a copy and paste error. I fixed it in the original.