I haven't looked for them in the past, but I think you could scoop a few from one of your friendly neighbourhood fast-food restaurants.  I can't remember the construction, but I think you could just undo the seam and then use some double-sided tape to put it back together or use some brads.  I will try to find some to buy and report back!

Can you buy clean fry boxes?

Cute idea!  I was just thinking that it might be easier to get some fry boxes and follow the instructions you posted for the take-away containers.