So what if a particle travels a tiny bit faster than light. Wasn't this Theory open to a little error anyways?
'Unified Field Theory' is what you are referring to. It attempts to 'unify' the 'fields' of 'Newtonian' and 'Quantum' physics. It was Einsteins theory, and even he had problems with it. (Quantum physics apparently work, and Newtons physics apparently work,; it just the unifying the very 'tiny' with the 'normal' size physics that is a problem.)
E=MC^2 is a different theory, and what is being debated with the neutrino experiment.