/*
 * Find an element within a page. Works with nested master pages, controls.
 */
function $(elementId, getElement) {
    getElement = !getElement ? document.getElementById : getElement; // default to document.getElementById
    var element = getElement(elementId);
    if (element != null) {
        return element;
    } else if (document.getElementById("bodyId") != null) {
        var rg = new RegExp("(?:id=\"?)((?:ctl00)(?:[\\$_]*))+(?:[^\\s>]*)(?:[\\$_])" + elementId);
        var values = rg.exec(document.getElementById("bodyId").innerHTML);
        return getElement(values != null ? values[0].replace("id=", "").replace("\"", "").replace(" ", "") : elementId);
    }
    return null;
}

Just give your body tag in the Master page an id and replace all references to "bodyId" in the above script to use that id.