You don't need to include the LOGIN or CONTENTPANE sections in the xml file. DNN will automatically parse those properly.
You only need one for the second contentpane and it has to have the runat/server setting included too:

<Object>
    <Token>[CONTENTPANE:1]</Token>
        <Settings>
            <Setting>
                <Name>id</Name>
                <Value>leftcontent</Value>
            </Setting>
            <Setting>
                 <Name>runat</Name>
                 <Value>server</Value>
            </Setting>
        </Settings>
</Object>

You're getting the Duplicate ID errors because, in your HTML file, you're making a div called "leftcontent" and DNN is using the same name from the token in your XML file to create the panes. The divs must have a unique ID, so you can't call a div something then have DNN make another div with the same name.
If you open the ascx file in your skin folder, you'll see what I mean... that you have something like this:

    <div id="leftcontent">
        <div id="leftcontent" runat="server"></div>
    </div>
    <div id="maincontent">
        <div id="contentpane" runat="server"></div>
    </div>

Maybe try changing you HTML to something like this:

<div id="wholecontainer">
    <div id="header">[LOGIN]</div>
    <div id="left">[CONTENTPANE:1]</div>
    <div id="maincontent">[CONTENTPANE]</div>
</div>