Ive been using Cloner a few times now to 'clone' sites... But oh my, not once with any theme has it ever copied everything. In fact, it hardly copies anything. It doesnt even work with WPMUs own themes? For a test, create a Upfront design on one site and try clone it with all its content and settings. It wont copy your default design, and it copies no site settings at all. It also does not copy custom post type media attachments?! It doesnt even copy users or activated plugin and theme settings... That must be the lamest 'cloner' I have ever used. Might as well redo the entire site manually.