1. Prep the new server: IIS & .NET 2.0 (make sure ASP.NET is enabled in IIS).
2. Install WebDir 4.0.1235.0 on the new server.
3. Using WebDir System Manager, create a new WebDir VS with the same name and setting as the one on the old server (the most important thing here is that the name be the same, you are going to override everything else).
4. Launch the WebDir website and make sure it works - don't move to step 5 until it is working.
5. Once the WebDir VS is working copy all the files from the WebDir4 folder over the files on the new server.
6. Launch the VS again and make sure it still works after the copy.
7. Update DNS or published URL to point to the new server.
8. Decommission old server.
That's it!