Untitled

Place div over Flash object with userscript
var myDiv= document.createElement("div");
myDiv.style.background = "red";
myDiv.style.width = "30px";
myDiv.style.height = "30px";
myDiv.style.position = "absolute";
myDiv.style.top = "0";
myDiv.style.left = "0";
document.body.appendChild(myDiv);

// code which apparently does nothing:
myDiv.style.zIndex = "999";
var swf_div = document.getElementById("swf_div");
if (swf_div) {
    swf_div.style.zIndex = "-999";
}

<body>
    ...
    <div id="client_div" style="width: 1680px; left: 0pt;">
        <object id="swf_div" width="100%" height="100%" type="application/x-shockwave-flash" data="http://c1.glitch.bz/swf/Boot_78793.swf" style="visibility: visible;">
            <param name="allowscriptaccess" value="always">
            <param name="allownetworking" value="all">
            <param name="wmode" value="direct">
            <param name="flashvars" value="--- auth tokens, omitted ---">
        </object>
    </div>
    ...
</body>

// code to create and style myDiv, see original question

document.addEventListener("DOMNodeInserted", nodeInserted, false);

function nodeInserted(e) {
    if (e.target.id == "swf_div") {

        var found = false;

        var params = e.target.getElementsByTagName("param");
        for (var i = 0; i < params.length; i++) {
            if (params[i].getAttribute("name") == "wmode") {
                var clone = params[i].cloneNode(true);
                clone.setAttribute("value", "opaque");
                params[i].parentNode.replaceChild(clone, params[i]);
                found = true;
                break;
            }
        }

        // in case swf_div doesn't already have a wmode param
        if (!found) {
            var clone = e.target.cloneNode(true);
            var param = document.createElement("param");
            param.setAttribute("name", "wmode");
            param.setAttribute("value", "opaque");
            clone.appendChild(param);
            e.target.parentNode.replaceChild(clone, e.target);
        }

        continueScript();
    }
}

function continueScript() {
    document.body.appendChild(myDiv);

    // do wonderful things
}