While I think it will be possible to do much of what you are wanting with enough time and manpower, there will be a lot of little things that will need to be changed to stop ANYONE from figuring out it's DNN.
You'd have to change the skin path, how the ClientID/UniqueID is generated, re-write some of the Core/Default modues (like search and breadcrumb) or not use them.
If your goal was to stop the casual user (or pretty much anyone not familiar with DNN), I think that goal is much simpler. The fixes I can think of to set it up this way, would be to edit (something in the core) to remove the DotNetNuke copyright notice in the HTML. In the Host menu - Uncheck - Show CopyRight Credits. Set the site up to use friendly URLs (really simple) which will prevent the "tabID" from showing most of the time. Following that, I have seen other Non DNN sites use TabID in the url.
Other thoughs...
Changing the namespaces would prevent you from using any 3rd party controls without access to the source code.
Changing DesktopModules would force you to re-write the module upload section. (changing skin path forces skin upload change)
I think the correct question to ask here is, "Why do they want to hide that they are using DNN?" If they want to hide the framework because of security, they can't hide that they are running a site using ASP on IIS. Using DNN without that level of modifications, will be faster and easier to upgrade to fix any security holes, that are found, than trying to include the changes into your modified code and test it, ect.
If it's an ego thing - they want it to look custom built - unless your skills in ASP.NET and with DNN specifically is expert level, I'd suspect it would be faster to actually build a custom solution. (I don't build custom frameworks or modify the core elements, well... not much) so I can't say for shurzies.
If you can get a "why" they want it with no DNN references, we might be able to better address that issue, either by changes in DNN, or recommending other solutions.