there is no tunnel btw, they are fired through the ground. Neutrino's are weakly interacting particles and travelling through the earth is like travelling through space for them, they will hardly interact at all.
the neutrinos are produced in bunches by producing Mesons from which they decay (pions or kions). The bunches are produced in a very similar way to the LHC bunches, in fact they come from the same initial accelerator, the SPS. Simply put, a bunch (~1x10^11 protons) of protons are fired into a target that will give off charged Mesons, Mesons of a certain energy are collected and focused with magnets into a decay tube. The decay length of these Mesons is well understood and so you will have a bunch of Mesons, all decaying in this tube and you can calculate the energy of the neutrino that will decay at a certain angle.
So the timing comes from the proton bunches, which is very well understood, the emitance of Mesons from the target is well understood as is their decay length and time. You won't know exactly how many neutrinos you are producing, but you will know at what time you are producing them and what type of neutrinos. This experiment wasn't built to measure the speed of neutrinos after all, it was built to measure neutrino oscillations, this measurement is a side project that put a spanner in the works.
They know these are neutrinos from the beam because of few features, firstly there is a bunch of them heading over so you'd get a splatter of hits over a certain time corresponding to the bunch size, secondly their energy is tuned to ~17 GeV and thirdly (and I'm assuming here) if the experiment is anything like other neutrino experiments they are pretty decent at being able to tell the general direction the neutrino was travelling. (all of this is in the paper I linked btw, I'm just giving the basic principles here, they go into detail on how they can measure the structure of the proton bunch at CERN and resolve a similar structure occuring in the neutrino signal at gran sasso.)
The accuracy of the beamline is measured to with 20cm, it is 731278.0, ± 0.2m
Thanks for the pic Yecti, loved it
The idea of the tunnel, this is totally nutty btw, (it won't happen unless they can't find anything wrong with the experiment), is so that they can fire a laser down the damn thing and get a more accurate measurement on the distance between the source and detector.
In regards to the distance, the 743km, again it has nothing to do with relativity, it is this distance because, a) CERN can produce a nice neutrino beam and b) it is a long enough distance for the neutrinos to start oscillating and be at one of the high mixing points (imagine a sine wave and choosing a distance where it's at its maxima) for the muon neutrinos to oscillate into electron neutrinos.