First of all, I think it is a definitely a smart move to begin transitioning to the new RadControls for ASP.NET AJAX. The new and improved architecture in this next gen control suite will help you build great projects for years to come.
That said, the upgrade process from "classic" controls to the new controls is not as simple as replacing assemblies. You do have to make some changes to your code to accommodate the new architecture of the ASP.NET AJAX-based controls. There are complete articles in the help for each control that will walk you through this process, so I'd suggest setting aside some time to address the issues you face in your project during the upgrade.
To get you started, here is the page that addresses RadMenu migration:
Hope this helps. Let me know if you get stuck.