Probably not a great help to you but using your desciption, the fact its not there with clutch in means it's probably not gearbox and if it wasn't there before, you can count out engine. That leaves clutch/flywheel area. Your milo tin comparison made me laugh but it also made me think it could be 1 or more broken/loose flywheel clutch drive straps (p/n

. The broken strap can scrape on housing or just rattle the ends together and as long as there's one atleast holding it, it probably wont rattle badly.
http://www.minispares.com/catalogues/cl ... spx?1~3~29