Creating a strong password with javascript

You can create a function that ensures your pwd contains at least one of a specific set of chars:

function ensurePwdContains(pwd, regexListOfChars, listOfChars) {
    if (!regexListOfChars.test(pwd)) {
        // select random char from listOfChars
        var newChar = listOfChars.charAt(Math.floor(Math.random() * listOfChars.length));

        // insert it into the current pwd in a random location
        // must do +1 to include the location at the end of the string
        var pos = Math.floor(Math.random() * (pwd.length + 1));
        pwd = pwd.slice(0, pos) + newChar + pwd.slice(pos);
    }
    return pwd;
}

This function will test to see if the password contains at least one instance of the regex passed in. If not, it will select a random character from the listOfChars argument and then insert that into the existing password in a random location.

And, then you call this function at the end of your function for each of your two cases:

FinalPwd = ensurePwdContains(FinalPwd, /[!#\$@*]/, sSpecialCharacters);
FinalPwd = ensurePwdContains(FinalPwd, /[A-Z]/, "ABCDEFGHIJKLMNOPQRSTUWXYZ");

Demo: http://jsfiddle.net/jfriend00/ur9FL/

And, here's a cleaned up version of your overall implementation. You were referring to a number of variables in your function that either aren't defined in your post or aren't used in your function so I removed those (since I don't know what they are or how they're used). Here's a bit cleaner implementation:

function generatePwd(minLen) {
    // create a pwd that is between minLen and ((2 * minLen) + 2) long
    // don't repeat any characters
    // require at least one special char and one capital char
    function rand(max) {
        return Math.floor(Math.random() * max);
    }

    function ensurePwdContains(pwd, regexListOfChars, listOfChars) {
        if (!regexListOfChars.test(pwd)) {
            var newChar = listOfChars.charAt(rand(listOfChars.length));
            var pos = rand(pwd.length + 1);
            pwd = pwd.slice(0, pos) + newChar + pwd.slice(pos);
        }
        return pwd;
    }

    var legalChars = "!#$@*123456789aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ";
    var specialChars = "!#$@*";
    var specialRegex = /[!#\$@*]/;
    var caps = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
    var capsRegex = /[A-Z]/;
    var nums = "123456789";
    var numRegex = /[1-9]/;

    // make legalChars into an array of chars (easier to deal with)
    legalChars = legalChars.split("");
    var pwd = "", len = minLen + rand(minLen), index;

    // ensure len is not too long
    len = Math.min(legalChars.length, len);

    // now add chars to the pwd string until it is of the desired length
    while (pwd.length < len) {
        index = rand(legalChars.length);
        pwd += legalChars[index];
        // remove the char we just used
        legalChars.splice(index, 1);
    }
    // ensure we have at least one special character and one caps char and one 1-9
    pwd = ensurePwdContains(pwd, specialRegex, specialChars);
    pwd = ensurePwdContains(pwd, capsRegex, caps);
    pwd = ensurePwdContains(pwd, numRegex, nums);
    return pwd;    
}

And, a working demo that generates a whole bunch of passwords so you can see what type of variation you get: http://jsfiddle.net/jfriend00/7dReY/

To put the password into place, I'd suggest you make a second function that calls the first function to generate the password and puts it into the field of choice:

function putPasswordInPlace(pwdId, sBtnName) {
     var pwd = generatePwd(8);
     document.getElementById(pwdId).value = pwd;
     EnableButton(sBtnName);
}