Just to go off on a completely different direction from the other suggestions, I have a similar clicking noise (like the spokey dokeys) which I have finally tracked down. It is the part of the OEM wind deflector that fills in the roll hoop on the left hand side. The plastic seems to be too loose and, as you have described, vibrates with the windows open or with the roof down but not with the car all closed up (as you would expect). I don't know if you have this part fitted but it's all I can think of.