One of the little gotchas to be aware of if you decided to choose the Gradual migration strategy affects pre-existing web applications. If you look at this screen shot:
After installing MOSS, successfully running through the Config Wizard and commencing a gradual migration, we see the following in the IIS Manager:
The problem with this is that any and all web applications such as our SPSWebApp that are installed into virtual directories under the Default Web Site also now have a new port under which they run. Since most web application references and code simply reference the URL without any port specification, IIS would default to port 80 on said web application requests. Given that the web application does not exist on port 80 anymore, such requests would fail with 404 errors.
So, be aware of this little gotcha. The way to work through this is to uninstall your web applications before you commence the gradual upgrade, but after the Config Wizard was done. Then once the new port 80 web site was created, reinstall your web applications to the Default Web Site_Pair web site on port 80.
That should about do it. J