// create a TreeWalker of all text nodes
var allTextNodes = document.createTreeWalker(document.body,NodeFilter.SHOW_TEXT),
    // some temp references for performance
    tmptxt,
    tmpnode,
    // compile the RE and cache the replace string, for performance
    cakeRE = /cake/g
    replaceValue = "pie";

// iterate through all text nodes
while (allTextNodes.nextNode()) {
    tmpnode = allTextNodes.currentNode;
    tmptxt = tmpnode.nodeValue;
    tmpnode.nodeValue = tmptxt.replace(cakeRE,replaceValue);
}

// the innerHTML property of any DOM node is a string
document.body.innerHTML = document.body.innerHTML.replace(/cake/g,'pie')

var search_re = new RegExp("(?:>[^<]*)(" + stringToReplace + ")(?:[^>]*<)", "gi");

// replace some chunk of stuff, the first section of your page works nicely
// if you happen to have that organization
//
setTimeout(function() { /* replace the rest */ }, 10);

var tmp = element.innerHTML.replace(search_re, whatever);
/* more replace calls, maybe this is in a for loop, i don't know what you're doing */
element.innerHTML = tmp;

$('body').html($('body').html().replace('pie','cake'));