One question: does the order of the pair ($word1, $word2) matter? In other words (making the same assumption as to what you mean as bobf above), is:

I will not

equivalent to:

will I not

for your purposes, or is it different?

Update: Since you say "I think I will be accessing these parings via the $word1-$word2 parings", why not use an HoH, with $word1 and $word2 stringified as the key to the outer hash, and populate it something like this:

# foreach group of three words
      $hash{$word1 . ' ' . $word2}{$word3}++;
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Or, more generally, for any number of words in your 'chain':

# foreach group of n words in array @n_words
      my $nth_word = pop @n_words;
      $hash{join ' ', @n_words}{$nth_word}++;
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And if the answer to my question in the first part of this post is that order doesn't matter, just change that last line to:

      $hash{join ' ', sort @n_words}{$nth_word}++;