I didn't test this but after a quick look here's what I think. Change this section in the "on main(pdfFile)" handler to the following...
-- Go through the sorted list, counting the instances of each word. Store each word and its score in a list in the 'scores' list in the script object above.
set wordsToIgnore to {"and", "the", "a", "for", "in", "is"}
set currentWord to item 1 of o's wrds
set c to 1
repeat with i from 2 to (count o's wrds)
set thisWord to item i of o's wrds
if thisWord is not in wordsToIgnore then
if (thisWord is currentWord) then
set c to c + 1
else
set end of o's scores to {currentWord, c}
set currentWord to thisWord
set c to 1
end if
end if
end repeat
set end of o's scores to {currentWord, c}