Cannot Convert Master Page to WAP

Question

I have a master page which when I try the "Convert to Web Application" command on it in VS 2008, it fails because of some user controls that it says it doesn't recognize. But I need this Master Page to work and to be converted because practically every other user control uses this master page and references some properties and other controls from it.

I have a namespace reference and register code at the top for those user controls in the master page but it still complains. So about the only thing I'm able to do is comment out those controls in the Master page then do a convert but then the designer file lacks references to those controls because I commented them out in the Master page.

No matter what I do I can't figure out a way to get this to convert successfully:

<%@ Master Language="C#" AutoEventWireup="true" CodeBehind="Main.master.cs" Inherits="sss.MasterPages_Main" %>
<%@ Register Src="Header.ascx" TagName="Header" TagPrefix="pmc" %>
<%@ Register Src="Footer.ascx" TagName="Footer" TagPrefix="pmc" %>
<%@ Register Src="Navbar.ascx" TagName="Navbar" TagPrefix="pmc" %>
<%@ Register TagPrefix="pm" Namespace="sss.Controls.Custom" %>

...and here is one of the tags referencing a control (it doesn't matter if it's a user or custom control, I get this issue on both references)

<tr>
    <td colspan=2 class="default-header"><pmc:Header ID="Header1" runat="server" /></td>
</tr>

The top part of Header.ascx.cs showing the namespace its in

namespace sss
{
    public partial class Header : System.Web.UI.UserControl
    {
        protected void Page_Load(object sender, EventArgs e)
        {

I have the namespace sss in the user control's code behind and this master page is also namespaced with sss (sss is our company name that I want to keep private in this post)

So I don't know what else to do. I'm working with 1500 errors all are like this but I need to get my Master Page converted and working first!