I know I'm getting in on this late, but I have ran into some of these issues also and let me share how I tackled some of them:
to create an Intranet portal for use by domain users only. I want DNN to recognize who is logged into Windows so that users do not need to login the the portal. I will be using group membership to restrict viewing of certain pages to certain groups.
Since we ghost all of our machines before we send them out, I change the settings in IE to automatically logon with current user login name and password. I set this by default and then the users will be logged on to the portal when they hit the page. That takes care of the automatic login for when a user is on campus and at their machine.
Incomplete user profiles in AD cause problems
If a user does not have email in AD (many of our users do not have email), the user is still created in DNN, but the email field is blank.
I deal with the same situation here. What I did to take care of this problem is that I added a SQL Trigger to the table that checks the fields after a user is created. If the Email or First/Last Names are blank the Trigger fires and updates the fields.
Ok, try not to fall down laughing over this one, very simple and it serves the purpose. I created an HTML page that does an automatic redirect to the login page. Set the priority of how pages are access in IIS and made sure that index.html was the first page that was accessed from that site.
Hope that helps some.
Steven