In picture 1 you have the air inlet temp sensor which will need to be put into the new pipe. By the way, the sensor is facing the wrong way. You need to turn it 90 degrees so that the clip is facing the airbox. Also to the right of the picture you have the fuel pressure regulator pipe (fpr). This will need to be relocated to the side of the inlet manifold where you will find a spare take off nipple which will probably have a black rubber cover on it. Be careful when removing it that you don't break anything.
In picture 2 you have the EGR pipe that will need to be removed and you can put a 2p in to the hole to blank it off with some sealant. You will also need to make yourself a blanking plate to cover the hole left on the head. There are threads on this mod available.
In picture 3 you have the cam cover breather pipe which you would run to your oil catch tank.