How do I ensure saved click coordinates can be reload to the same place, even if the page layout changed?

Yeah, there are many, many ways a page’s layout can alter between loads. Different window sizes, different font sizes, different font availability, different browser/settings (even a small change in layout or font preference can throw out the wrapping). Storing page-relative co-ordinates is unlikely to be that useful unless your page is almost entirely fixed-size images.

You could try looking up the ancestors of the clicked element to find the nearest easily-identifiable one, then make a plot from that element down to the element you want based on which child number it is.

Example using simple XPath syntax:

document.onclick= function(event) {
    if (event===undefined) event= window.event;                     // IE hack
    var target="target" in event? event.target : event.srcElement; // another IE hack

    var root= document.compatMode==='CSS1Compat'? document.documentElement : document.body;
    var mxy= [event.clientX+root.scrollLeft, event.clientY+root.scrollTop];

    var path= getPathTo(target);
    var txy= getPageXY(target);
    alert('Clicked element '+path+' offset '+(mxy[0]-txy[0])+', '+(mxy[1]-txy[1]));
}

function getPathTo(element) {
    if (element.id!=='')
        return 'id("'+element.id+'")';
    if (element===document.body)
        return element.tagName;

    var ix= 0;
    var siblings= element.parentNode.childNodes;
    for (var i= 0; i<siblings.length; i++) {
        var sibling= siblings[i];
        if (sibling===element)
            return getPathTo(element.parentNode)+"https://stackoverflow.com/"+element.tagName+'['+(ix+1)+']';
        if (sibling.nodeType===1 && sibling.tagName===element.tagName)
            ix++;
    }
}

function getPageXY(element) {
    var x= 0, y= 0;
    while (element) {
        x+= element.offsetLeft;
        y+= element.offsetTop;
        element= element.offsetParent;
    }
    return [x, y];
}

You can see it in action using this JSFiddle: http://jsfiddle.net/luisperezphd/L8pXL/