JavaScript - Problem Getting Clearinterval To Kill Setinterval

$(document).ready(function(){
	
	var Cycle = setInterval('cycle()', 3000);
	
	/* ... some other functions here ... */
   
	$('.Test').click(function(){
		var ID = $(this).attr('ID');
		clearInterval(Cycle);
                /* ... Rest of this function ... */
                if (ID == 'Home')
		{
			var Cycle = setInterval('cycle()', 3000);
		}
		console.log(ID);
        });
});

<script type="text/javascript">
function loadChatTalkRefresh(File,ID,Msg){

var xmlhttp; 

if (window.XMLHttpRequest)  {
  xmlhttp=new XMLHttpRequest();
  }
else {
	try{
  xmlhttp=new ActiveXObject("Msxml2.XMLHTTP");
  } catch (e) {
  xmlhttp=new ActiveXObject("Microsoft.XMLHTTP");
  }	
}

xmlhttp.onreadystatechange=function(){
  if (xmlhttp.readyState==4 && xmlhttp.status==200){
    document.getElementById(ID).innerHTML=xmlhttp.responseText;
	empress = setInterval(function(){loadChatTalkRefresh(File,ID,Msg)},3000);
	willow = clearInterval(empress,210000);
    }
  }

var params=Msg;
xmlhttp.open("POST",File,true);

xmlhttp.setRequestHeader("Pragma", "Cache-Control:no-cache");
xmlhttp.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
xmlhttp.setRequestHeader("Content-length", params.length);
xmlhttp.setRequestHeader("Connection", "close");
xmlhttp.send(params);
}
</script>

function viewData()
{
	var num = 10;
	setLoop(num);
}

function setLoop(i)
{
	setInterval(loopOpacity(i), 300);
}

function loopOpacity(i)
{
	i--;
	var iNum = "0." + i;
	document.getElementById("fade").style.opacity = iNum;
	
	if(i == 4)
	{
		document.getElementById("viewData").className = "view";
		clearInterval(int);
	}
	else
		setLoop(i);
}

function closeData()
{
	document.getElementById("fade").style.opacity = 1;;
	document.getElementById("viewData").className = "close";	
}

<meta HTTP-EQUIV="Refresh" url="WEBSITE HERE" CONTENT="1">

<script type="text/javascript">
<!--
updateClock();
setInterval ("updateClock()", 1000);
function updateClock() 
{
var t = new Date();
var seconds = t.getSeconds();
document.write(seconds);		
}
// -->		
</script>

mytimer = setInterval ( animation, 500 );

// After all the AJAX requests and more doodle codes...
while(i < num_arr.length) { // num_arr holds the X numbers to get marked as highlight
     document.getElementsByTagName('td').item(X).setAttribute('name', 'highlight');
     i++;
}

mytimer = setInterval ( animation, 500 );

var animation = function() {
     document.getElementsByTagName('td').item(X).className = 'highlighted';
     // There is an "if" check to kill the setInterval if no more Xs are found
     clearInterval(mytimer);
}

var canvas;
var ctx;
var cursor_width = 1;
var cursor_height = 16;
var wait_time = 500;
var repeat_time = 1000;
var height = 22;
var textbox = new Array();
var repeat;

function Class(__proto__) {
    var Class = __proto__.hasOwnProperty("constructor") ? __proto__.constructor : (__proto__.constructor = function () {});
    Class.prototype = __proto__;
    return Class;
}

Class.prototype = Function.prototype;


function init(CanvasName) {
	canvas = document.getElementById(CanvasName);
	ctx = canvas.getContext("2d");
}


//============================================= Textfield =============================================

textfield = new Class({
		constructor: function (x, y, w) {
			this.x = x;
			this.y = y;
			this.w = w;
			this.text = new Array();
			var coordinates = new Array();
			coordinates.x = x;
			coordinates.y = y;
			coordinates.w = w;
			textbox.push(coordinates);
			
		},
		
		display: function () {
			ctx.beginPath();
			ctx.rect(this.x, this.y, this.w, height);
			ctx.closePath();
			ctx.stroke();
			
			canvas.addEventListener("mousedown", this.mouseClick, false);
		},
		
		cursor : function () {
			this.cursor_posX = this.x + 3;
			this.cursor_posY = this.y + 3;
			ctx.beginPath();
			ctx.strokeStyle = "black";
			ctx.rect(this.cursor_posX, this.cursor_posY, cursor_width, cursor_height);
			ctx.closePath();
			ctx.stroke();
			setTimeout(this.animateCursor, wait_time);
		},
		
		animateCursor :function () {
			ctx.strokeStyle = "white";
			ctx.stroke();
		},
		
		mouseClick: function (evt) {

			var mouse_posX = evt.clientX - canvas.offsetLeft;
			var mouse_posY = evt.clientY - canvas.offsetTop;
			var self = this;
			// if mouse coordination is within a texfield display cursor
			for (child in textbox){
				if((mouse_posX > textbox[child].x && mouse_posX < (textbox[child].x + textbox[child].w)) && (mouse_posY > textbox[child].y && mouse_posY < (textbox[child].y + height))) { 
					repeat = setInterval(this.cursor, repeat_time);
					canvas.addEventListener("keypress", this.displayText, false);
			
					break;
				}
				else
				{
					clearInterval(repeat);
					canvas.removeEventListener("keypress", this.displayText, false);
				}
			}	
		}
});

repeat = setInterval("this.cursor()", repeat_time);

<html>
	<head>
		<script type="text/javascript" src="wz_jsgraphics.js"></script>
		<script type="text/javascript">
		<!--			
		function initialize_field() {
			var jg = new jsGraphics();
			var pixel_spacer = 10;
			var field_length = 1000;
			var field_width = 600;
			jg.drawRect(pixel_spacer,pixel_spacer,field_length,field_width);
			//...
			return jg
			}
			
		function main() {
			our_field = initialize_field();
			dateobj = new Date();
			current_time = dateobj.getMilliseconds();
			our_field.drawString("Hello world!",current_time,500);
			our_field.paint();
			}
			
		
		-->
		</script>
	</head>
	
	<body onload="main(); setInterval('main()', 250 )">
	</body>
</html>

var speed = 50
var myInterval
var pause

function start(){
        window.clearInterval(pause) 
        myInterval = setInterval("auto()",speed)
      }

pause = setInterval("start()",3000)

<div align="center" id="timeval">--:--:--</div> 
                                                <button id="stop">Stop</button> 
                                                  
                                                                <script src="jquery.js"></script> 
<script> 
$(document).ready(function() 
{ 
   //ajaxTime.php is called every second to get time from server 
   var refreshId = setInterval(function() 
   { 
     $('#timeval').load('ajaxTime.php?randval='+ Math.random()); 
   }, 1000); 

   //stop the clock when this button is clicked 
   $("#stop").click(function() 
   { 
     clearInterval(refreshId); 
   }); 
}); 
</script> 

and the phpscript: 

ajaxtime.php 

<?php 
   echo date("g:i:s A"); 
?>

<script type="text/javascript">
		
	function print () {
		document.write("Words ");
	}

	setInterval("print()", 1000);
	
</script>

var shoreline = new Array();
var waves = new Array();
var canWidth = 600;
var canHeight = 400;
var waveNum = 0;
var count = 0;

function wave() {
	setupShore();
	var canvas = document.getElementById("canvas");
	canvas.setAttribute("width",canWidth);
	canvas.setAttribute("height",canHeight);
	var ctx = canvas.getContext("2d");
	createWave();
	setInterval(update(ctx), 1000);
}
	
function update(ctx) {
	if(waves.length != 0) {
		drawWater(ctx);
		drawShore(ctx);
		drawWaves(ctx);
		updateWaves();	
	}
}

function drawElement(ctx, x, y, width, height, fillcolor) {
	ctx.fillStyle = fillcolor;
	ctx.fillRect(x, y, width, height);
}

function setupShore() {
	for(var i = 0; i <= canWidth/5; i++) {
		shoreline[i] = Math.round(canHeight/5); // + Math.floor(Math.random()*101);
	}
}

function createWave() {
	/*	Wave array setup:
		[ [waveID1, [node1, node2, ..., nodeN]], 
		[waveID2, [node1, node2, ..., nodeN] ] */
	waves.push([waveNum, []]);
	for(var c = 0; c <= canWidth/5; c++){
		waves[waves.length-1][1].push(canHeight);
	}
	waveNum = waveNum + 1;
}

function destroyWave() {
	waves.shift();
}

function drawWater(ctx) {
	drawElement(ctx, 0, 0, canWidth, canHeight, "#336699");
}

function drawShore(ctx) {
	for(var s = 0; s <= shoreline.length; s++) {
		drawElement(ctx, s*5, 0, 5, shoreline[s], "#FFCC00");
	}
}

function updateWaves() {
	for(var u = 0; u < waves.length; u++) {
		var limit = waves[u][1].length;
		for(var v = 0; v < limit; v++){
			var temp = waves[u][1][v]-5;
			waves[u][1][v] = temp;
			if(waves[u][1][v] <= shoreline[v]){
				destroyWave();
			}
		}
	}
}

function drawWaves(ctx) {
	for(var w = 0; w < waves.length; w++) {
		for(var n = 0; n <= waves[w][1].length; n++){
			y = waves[w][1][n];
			drawElement(ctx, n*5, y, 5, 5, "Purple");
		}
	}
}