Here is a small AppleScript for counting the words of a PDF file from Skim.
tell application "Skim"
set PDFwords to 0
set numberOfMyPages to count pages of document 1
repeat with currentPage from 1 to numberOfMyPages
set numberOfPageWords to count words of page currentPage of document 1
set PDFwords to PDFwords + numberOfPageWords
end repeat
display dialog "Number of words: " & PDFwords buttons {"Cancel", "OK"} default button 2
end tell
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