right just had a look at my focus.
sorry my bad, the whole in your second pic is definately for the brake servo.
1, goes up and round to the charcoal canister (i'm prob totally wrong with that so heres a pic). its the small pipe at the top with the rubber sleeve.
your 2 is different to mine. i have a bit of platic sticking out of my manifold the right size to accept that size of pipe but the end hasnt been chopped off so its blanked off from factory. however i do have a bigger ipe with a clip directly above that pipe and slightly higher than the other two. heres a pic
an that goes to the same thing number 1 does but its a bit lower down, see my first pic (not the thing with green on it in the back ground, its the weird clippy thing)
3 for me disappears by the alternator and comes up between the alternator and block to the fuel pressure regulator.
hope that help, the only difference between my 2l focus and that mondeo inlet is no. 2. 8)