If you can take advantage of iframes, much of your problem is solved already, iframes display a unique page within its shortened and narrowed parameters, and since you don't have to necessarily have borders or scrollbars, no one but you, the designer need be the wiser.

Another method would be to find every instance of names referring to your javascript in your page and in how each menu is made, and rename them, but all of the renaming would not work unless you find all instances of how they call out each other in the script. It could work in theory, but the method above does not require any renaming and may be infinitely easier.