Not sure if this will solve it for you but I had a similar circumstance.  I built a new server (hardware), installed the OS (windows 2003 server standard) and then from there did everything via Remote Desktop.  I followed the DNN installation instructions (along with my notes from previous installs), created a DB, unzipped DNN, adjusted the web.config and then tried to access DNN via a web browser.  All I could get was a 404 error. 

I read through some other postings on this forum and someone suggested that .NET 2.0 wasn't installed properly.  I remember that I did a windows update before I installed IIS (it is not part of the default install) and the windows update installed .NET 2.0.  So the order went Windows, Windows Update (including .NET 2.0), and then IIS.  I did what was suggested in the other post and did an add/remove programs, .net 2.0, repair.  Everything worked after that.

Perhaps this will help, perhaps not but for me the moral of the story is to always install IIS before updating windows to include .NET 2.0.

Ted

There should be no problem using remote desktop to do the install.  You will want to make sure that default.aspx is set as your default page.  You will also want to make sure that ASP.NET 2.0 is selected as the .NET version for your website.  You also might need to register ASP.NET in IIS using the aspnet_regiis.exe tool.