Definately, otherwise it would have one less tooth....
Don't think the Amal valve has got anything to do with your issues though, and as you have stated you think it's the airbox side anway.
CPS or "Crank position sensor", and Phase sensor are NOTORIOUS to fcuk on all cossies, and being that a new CPS is only £20 i'd get one ASAP, since you say it's already got a new phase sensor on it.