Since the OP asked for a way to replace all the duplicate id's before appending them, maybe something like this would work. Assuming you wanted to clone MainConfig_1 in an HTML block such as this:
<div id="smallConfig">
<div id="MainConfig_1">
<ul>
<li id="red_1">red</li>
<li id="blue_1">blue</li>
</ul>
</div>
</div>
The code could be something like the following, to find all child elements (and descendants) of the cloned block, and modify their id's using a counter:
var cur_num = 1; // Counter used previously.
//...
var cloned = $("#MainConfig_" + cur_num).clone(true, true).get(0);
++cur_num;
cloned.id = "MainConfig_" + cur_num; // Change the div itself.
$(cloned).find("*").each(function(index, element) { // And all inner elements.
if(element.id)
{
var matches = element.id.match(/(.+)_\d+/);
if(matches && matches.length >= 2) // Captures start at [1].
element.id = matches[1] + "_" + cur_num;
}
});
$(cloned).appendTo($("#smallConfig"));
To create new HTML like this:
<div id="smallConfig">
<div id="MainConfig_1">
<ul>
<li id="red_1">red</li>
<li id="blue_1">blue</li>
</ul>
</div>
<div id="MainConfig_2">
<ul>
<li id="red_2">red</li>
<li id="blue_2">blue</li>
</ul>
</div>
</div>