Here are the relevant pictures from the manual.
The throttle cable is the upper of the two (arrowed) in the third photo. No idea what the second cable is - there isn't one on my Evo!
It runs between the brake hoses and the headstock then in front of the wiring coloured green in the photo. Then it's between the frame and airbox (passing through the loop on the side of the airbox) and on to the throttle quadrant.
Hope that helps.