Sure, you can achieve this by splitting the string into words, reversing the order of the words, and then joining them back together. Here's a JavaScript function to do that without using any built-in functions:

```javascript
function reverseWords(str) {
    let reversedStr = ''; // Initialize an empty string to store the reversed string
    let word = ''; // Initialize an empty string to store each word temporarily
    let words = []; // Array to store all the words

    // Loop through each character in the string
    for (let i = 0; i < str.length; i++) {
        // If the character is not a space, add it to the temporary word string
        if (str[i] !== ' ') {
            word += str[i];
        } else {
            // If the character is a space, push the temporary word to the array and reset the word string
            words.push(word);
            word = '';
        }
    }
    // Push the last word to the array
    words.push(word);

    // Loop through the array of words in reverse order and concatenate them to form the reversed string
    for (let j = words.length - 1; j >= 0; j--) {
        reversedStr += words[j];
        // Add a space between words except for the last word
        if (j !== 0) {
            reversedStr += ' ';
        }
    }

    return reversedStr;
}

// Example usage:
const inputString = "Sky is the limit";
console.log(reverseWords(inputString)); // Output: "limit the is Sky"
```

This function iterates through the characters of the input string, builds each word, stores them in an array, then constructs the reversed string by concatenating words in reverse order.