Have you checked all of nuts and bolt are done up tight on the accessories attached to the bike; panniers, mudguard, chainguard etc. Or maybe your gears aren't clicking in smoothly, might need adjusting?
It sounds like something is clicking as it is being put under strain. I would suggest it is something in or around the motor seeing as this is where most of the weight will end up from pushing down on the handlebars. Is the bike still under warranty?
Bungee
Will certainly look out for those! Just when I have nearly done up the second hook the first one pings off and smacks me. What a great post, Thanks