After creating the code for random ball generator, removeral and hit detection it was relatively simple to replicate the code for each of the three types of ball I have decided to use. The variables used had to be changed to prevent conflicts between the various parts of the code.

I added code to freeze the game once the timer reaches zero:

if ((count)-myTimer.currentCount == 0){
finalscoreTxt.text = "You scored " + String(score);
gameState = "finished";
ballP1.alpha = 0.5;
}

The frequency of which the code generates different types of balls was balanced:

setInterval(ballGenGOOD,100);
setInterval(ballGenBAD,500);
setInterval(ballGenBONUS,10000);

The interval time for the bonus ball was later randomised and effected by an external rss feed.

A play again button was added which is moved from outside of the stage once the timer reaches zero:

function playagain(event:MouseEvent):void {
countTxt.text = time;
againTxt.y = 700;
finalscoreTxt.text = "";
ballP1.alpha = 1;
gameState = "started"
score = 0;

var count:Number = time;
var myTimer:Timer = new Timer(1000,count);
myTimer.addEventListener(TimerEvent.TIMER, countdown);
myTimer.start();
function countdown(event:TimerEvent):void{
countTxt.text = String((count)-myTimer.currentCount);
}