Though this is a large project, it can still be done in small steps. The first step could be a policy that all core functionality should be in separate methods, without changing the class structure at first.
For example, OFS.Folder.manage_addFolder() both creates and adds a folder, and also returns the HTML for the main management screen. manage_addFolder() could be refactored to first call a _createFolder() method (implementing the core functionality), and then return the HTML. With no changes in API or class structure, such refactoring can proceed now, as no existing code that uses manage_addFolder() would be affected.
In addition, we'd quickly get useful core functionality methods such as _createFolder(), which would become the preferred way of creating folders from Python code.
Then, for Zope 3.0, you can do the big class restructuring of moving the HTML rendering out of the core Folder class. This in turn will be easier because you will have already separated out the functionality into different methods.