This is the beauty of the web- the transition to a sane architecture can be done page by page- without any visibility to the user. Every time you have to make a change- fix an old feature or add a new one, you replace it with the new architecture. Even if it's not a whole page- you can load in a partial with javascript. The challenge is holding back from going too deep on the refactoring all at once. Functional tests around the system have to be added to keep your sanity as part of the change process.