I've seen implementations on other systems where this has been solved by placing a vertical bar to the right of the window. The height of this bar represents the total length of the document. Inside this vertical bar is a small bar which represents the current viewing window on the document. The user can "scroll" this small bar to move the current viewport over the large document.

I think I might start overriding the existing methods which users are used to with this method because I've build websites for a couple of years and think I know better than years of UI development by much more experienced people than I.