Well it seems like you have exhausted all of the common things to check. The only other thing that I can think of, is there are two fusible links associated with the charging system that exit from the power distribution box in the engine compartment, that you can check.
My only recommendation, at this point, is to carefully inspect all of the wiring and battery cables for any signs of damage. It would be helpful to have a wiring schematic that is specific for your car so you can more easily check the circuits that are most likely to cause a problem.
Or, perhaps, you can find a reputable shop nearby, that specializes in diagnosing automotive electrical systems.