You find any experts around, let us know. We'll do what we can to run 'em off! (ex=has been spert=drip under pressure)
Any other issue notwithstanding, removing the airbox lid will reduce the pressure differential that the carb runs on which will effectively result in a more lean A/F (air/fuel) mixture.
You mention not knowing what your current jetset is. There is the possibility in that case that less fuel could damage your motorcycle. The chance of that is slim, cuz it's unlikely your bike is jetted right on now.
Placing the CDI unit any place secure is fine. Don't stretch/kink/stress the wiring. Don't let it flop around. A tie-wrap will work. Using an existing threaded hole or making a new one will work, too.
It's not just the pilot that's effected in this case. Removing the lid will effectively lean every circuit. There is no replacement for the individual rider jetting his personal bike.
I hope you post the resolution to the 'bike won't run' that started this thread.