Without meaning to trivialise the issue in any way, it seems to me that a rewrite of WindowsSignin.aspx might be the easiest way to achieve a seamless login. That way you dont need to modify the core in any way; rather just point the site at WindowsSigninCustom.aspx. It also means that you don't need to work through the authentication stuff.
I'm faced with a similar problem and have decided to look at one of two alternatives:
1. Grab the Windows Login info and then query an (imported) database (from MS Exchange) (the only valid store of User data). The advantage here is the ability to pick up Group information based on standard Email groups;
or
2. Using CDO, query the Exchange Server to determine the user ID.
In both cases I dont need a password, as the User has already been authenticated through their standard Windows login.
I might point out that our use of AD (a historical problem) is rubbish and therefore I need to look at workarounds.
HTH in some way.
Steve T