Jquery :: Conflict Between Libraries - Mootools And Prototype

I have been trying in vain for many days to resolve a conflict between javascript libraries. My homepage uses jquery horizontal css menubar + a combined mootool and prototype accordian type sliding information box in the middle of the webpage. I find that the highlighter of the css menubar does not work when prototype.js is also loaded on the same page. I have read somewhere that $ should be replaced however I have tried every possible option and none works. I have jquery loading first as it is on my template, with this:
<script type='text/javascript' src='../Web/Templates/jquery-1.3.2.js'></script>
<script type='text/javascript' src='js/example.js'></script>

And my mootool and prototype loades further below like this:
<script type="text/javascript" src="scripts/intro/prototype.lite.js"></script>
<script type="text/javascript" src="scripts/intro/moo.fx.js"></script>
<script type="text/javascript" src="scripts/intro/moo.fx.pack.js"></script>
<script type="text/javascript">
function init(){
var stretchers = document.getElementsByClassName('box');
var toggles = document.getElementsByClassName('tab');
var myAccordion = new fx.Accordion(
toggles, stretchers, {opacity: false, height: true, duration: 600}
);
//hash functions
var found = false;
toggles.each(function(h3, i){
var div = Element.find(h3, 'nextSibling');
if (window.location.href.indexOf(h3.title) > 0) {
myAccordion.showThisHideOpen(div);
found = true;
}
});
if (!found) myAccordion.showThisHideOpen(stretchers[0]);
}
</script>