I agree with your concern too. I worked for a small animal veterinarian and helped put animals under for surgery. My hope is to get the birds unconscious place them in the cone and bleed them before they come to. They are using this method with hogs with great results. I will try the gassing but if it doesn't work well I will skip this step and just bleed the bird in a cone.
You may want to look into some of the commercial boxes made for euthanizing baby piglets. The problem that I have seen with them is that they are fairly difficult to maintain, at least on the farm, as they have to be constantly filled with gas and leak while taking animals in and out. I guess the constant thing is not really an issue if you're only using it on the day of slaughter.
I am going to try debraining this batch. I also thought about making an electrical stunning pool but am very concerned about (my) safety, so have put that on the back burner for now. I personally feel that decapitation is much less humane due to the large amount of research showing that decapitated animals have functional EEG waves for a significant length of time, with a huge pain response when the spinal cord is severed- in fact in the near future, this will likely no longer be a humane method of euthanasia for lab animals and I think its something that needs to be re-considered for home processing as well.
Let me know if your stunning box works out because I would be VERY interested in this.