I changed the two throttle cables this weekend and when I had removed the air box, I noticed that the previous owner had replaced the IAT sensor but didn't remove the old one in the air box and just has the new one laying there on top of some hoses and wiring. The 03' CBR954RR runs top notch but shouldn't the IAT sensor be screwed into the air box?

 

Yes. It's supposed to read the temperature of the air inside the intake, and faster moving air is cooler. Being outside makes it think the temperature is warmer than it is. I would think that this would be a bad thing, but maybe it isn't.