I just did a clean install of 4.0.962.0 on a clean build of Win 2008.
Created an IIS website with it's own application pool. Home dir is D:\Sites\MySite\
Set the application pool to .NET 4
Set the pool to run as a specific user
Made sure app pool user has full control to D:\Sites\MySite
Website uses host headers for www.mysite.com and mysite.com.
Create a new project using Project Manager
Go to IIS
Provide name of cms and path of D:\Sites\MySite\cms
Browse to new site and setup database on SQL Server with Windows Authentication
Browse to Admin site, login
Create New Page
Click "Create and go to add content"
I get a popup "IIS 7.0 Detailed Error - 404.6"