String index out of range: -1 within a crowded 'if' statement

I'm running a program that parses the text off of a website and then spell checks a string containing all of the text after it's been cleaned from HTML mark up.

Once the spell checker reaches the end of the string, it returns this this exception. I saw similar questions which were resolved by setting the index greater than 0 in an "if" statement, but I've been struggling to fix this for some time now and would appreciate some help in figuring this out.

Exception thrown:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
    at java.lang.String.substring(Unknown Source)
    at ParseCleanCheck.checkWord(ParseCleanCheck.java:173)
    at ParseCleanCheck.SpellChecker(ParseCleanCheck.java:101)

Java line 173-175 is where the word is stripped of any punctuation marks:

if (length > 2 && word.substring(length - 2).equals(",\"") || word.substring(length - 2).equals(".\"")
                || word.substring(length - 2).equals("?\"") || word.substring(length - 2).equals("!\"")) {
            unpunctWord = word.substring(0, length - 2);

Line 101 is documented below, I've added the relevant surrounding code that might be part of the exception being thrown

String user_text = "";
user_text = cleanString;
while (!user_text.equalsIgnoreCase("q")) {
                // check if necessary or if cleanString still works
                // PageScanner();
                user_text = cleanString;
                String[] words = user_text.split(" ");

                int error = 0;

                for (String word : words) {
                    suggestWord = true; // ~~~ Line 101 ~~~~
                    String outputWord = checkWord(word);

                    if (suggestWord) {
                        System.out.println("Suggestions for " + word + " are:  " + suggest.correct(outputWord) + "\n");
                        error++;
                    }
                }

                if (error == 0 & !user_text.equalsIgnoreCase("q")) {
                    System.out.println("No mistakes found");
                }
            }

        } catch (IOException e) {
            e.printStackTrace();
            System.exit(-1);
        }