gistfile1.js

var converter = (function () {
  'use strict';

  var romanNumeralsArray = [
      {roman: 'I', number: 1},
      {roman: 'V', number: 5},
      {roman: 'X', number: 10},
      {roman: 'L', number: 50},
      {roman: 'C', number: 100},
      {roman: 'D', number: 500},
      {roman: 'M', number: 1000}
  ],
  length = romanNumeralsArray.length,
  outputString = '',
  inputNumber = 0;
  
  //helper to get index of item in roman numeral array
  function getIndexOfLetterInNumeralsArray(strValue) {
    var i, obj;
    for (i = 0; i < length; i += 1) {
      if (romanNumeralsArray[i].roman === strValue) {
        obj = romanNumeralsArray[i];
        return romanNumeralsArray.indexOf(obj);
      }
    }
    return -1;
  }
  
  function romanNumeralGenerator(intVal, stringVal) {
    var i,
        matchedNumberIndex,
        matchedNumber = 0;

    //break condition for the recursive calls
    if (intVal < 1 || intVal > 3999) {
      return stringVal;
    }

    //iterate through numerals array to find the highest number that goes into the input
    for (i = 0; i < length; i += 1) {
      if (romanNumeralsArray[i].number <= intVal && romanNumeralsArray[i].number > matchedNumber) {
        matchedNumber = romanNumeralsArray[i].number;
        matchedNumberIndex = i;
      }
    }

    //add corresponding letter to the answer and subtract the number from the input
    stringVal += romanNumeralsArray[matchedNumberIndex].roman;
    intVal = intVal - matchedNumber;

    //recurse
    stringVal = romanNumeralGenerator(intVal, stringVal);
    return stringVal;
  }
  
  function amendOutput(input) {
    var i,
        output = '',
        match = input.match(/(.)\1{3}/g),
        allMatches,
        matchedCharacter,        
        //info from the input string
        repeatingCharFirstPosition,
        repeatingCharPreceedingChar,        
        //indices of the above characters in the numerals array
        rindex, pindex;

    //is there a character repeating 4 times?
    if (match) {
      allMatches = input.match(/(.)\1{3}/g).toString().split(',');
  
      for (i = 0; i < allMatches.length; i += 1) {
      	
        matchedCharacter = allMatches[i].split('')[0],
      	repeatingCharFirstPosition = input.indexOf(matchedCharacter),
      	repeatingCharPreceedingChar = input.split('')[repeatingCharFirstPosition - 1],
      	rindex = getIndexOfLetterInNumeralsArray(matchedCharacter),
      	pindex = getIndexOfLetterInNumeralsArray(repeatingCharPreceedingChar);
  
        //if the character preceeding the repeating one is the next numeral up
        if (pindex === (rindex + 1)) {
          output = output.substring(0, repeatingCharFirstPosition - 1);
  
          //if this is the first pass through fixing the string
          if (!output) {
            output = input.substring(0, repeatingCharFirstPosition - 1);
          }
          output += matchedCharacter + romanNumeralsArray[rindex + 2].roman;
        } else {
          output += matchedCharacter + romanNumeralsArray[rindex + 1].roman;
        }
      }
      input = output;
    }
    return {
      romanNumeralGenerator: romanNumeralGenerator
    };
  }
}());

I didn't make my code too clear...

You're on the right lines, but because I split the answer into 2 separate functions, and what with my lack of cleanliness in the code in general, the return should be like..

return {
  romanNumeralGenerator: function (input) {
    var answer = '';
    answer = romanNumeralGenerator(input, answer);
    answer = amendOutput(answer);
    return answer;
  }
}

Ah that makes more sense. There's a small chance I only skimmed your code!