Mass and spacetime may be indepdenent, but mass only expresses itself through spacetime, am I right? The current ideas on mass is that it is not an interaction with spacetime that determines mass, but the mass does directly determine how much that partical warps the fabric of space.
However, be it string vibrations or the Higgs field, these things have to happen in a dimension, especially in string theory, so I would have to say as they are independent, no understanding of it as we currently have shows it can exist without a spacial dimension. Even in the old point particle model, you still have a field right? so I would say mass cannot exist without spacetime, but I would take that further, that without space, there is no matter.
Quantum mechanics shows that energy and matter can spontaneously appear and disappear in the tinest of distances, so to say they are independent is a bit hasty.
E=MC^2 shows that they are related, but not neccesarily the same thing. However string theory would suggest that matter is closely related to energy, but related is not the same as saying they are the same thing.
Energy it appears did exist before space/time, as something kicked off the Big Bang, but of course again things get more interesting with string theory as the concept of distance as we know it go out the window in certain circumstances, one of them being the condition of the universe at the Big Bang.
Staying in the world of strings, we can at least answer one of those fundamental questions, and we know how small is the smallest thing, but if String Theory is totally wrong then we are back to square one.