A rubber band or "Rangerband" (rubberband made from bycicle innertube) would be good for holding the handles closed. To keep the cup on the nalgene bottle you can use a bandanna or even another rangerband depending on the size.

By the way, I don't know if Doug reccomends a metal cup in any of his kits, however it might might be something to look into. I have found it to be an indespensable item. It gets a lot of use.