1) And does, for example, the law of gravitation operate in a universe without a distinct force of gravity?
2) Bell's theorem is a rather unique bit of physics. The derived inequality is a precise mathematical consequence of three assumptions, logic, causality and realism (the local realism limitation was a restriction only of technique, 'strong Bell's' accounts for non-local realism also). You might also like to ponder why special relativity demands local realism in the first place.
http://www.nature.com/nature/journal/v446/n7138/abs/nature05677.html
Bell's inequality has been empirically shown not to be true, so we presume one of the three assumptions is wrong. Traditionally we like to believe the universe behaves logically and that effects never preceed causes, so we reject reality as the false assumption. Acausality is accepted so that causality and logic can abide.
Of course you don't have to accept that choice, you can instead reject causality and have a real, deterministic and logical universe, albeit one in which we see the effects of things that have not happened yet.
Or perhaps logic is not to your taste? We may then inhabit a universe where everything has a cause and causes never follow effects. And where if A is true or B is true then A and B are false.
There is acausality, there is no causality or the universe is fundementally illogical. That is a mathematical certainty. Not lightly has Bell's theorem been called "the most profound theorem in science".
3) General Relativity can be formulated as a gauge theory and usually is for matters of cosmology. Maybe you can explain to me how you demonstrated that the universe is a system from which neither matter nor energy enters or leaves? This being a precondition for the 2LOT to apply.
4) We have reasons to believe that the laws of physics of the universe today do not apply to the early universe, for a start not all of the forces or particles we know existed then. There are reasons why cosmologists don't just 'roll the clock back' beyond a certain point and say for sure that the universe began like so, it's because we don't know.
If you are really interested, "Physics of the Early Universe" - edited by J.A. Peacock, A.F. Heavens[*] , and A.T. Davies is available on Google Book Search. I believe it also has a section on basic gauge theory.
http://books.google.com
[* Surely not! :-)]