Your sentence "All Godel's incompleteness theorems says is that there will be open questions about a universe describable by finitely many rules" shows right there that there cannot be a theory of everything. How can you have a theory of everything yet still have open questions? That means that you have not answered everything.
For example, if everything in the universe obeyed Newtonian mechanics, I would say that Newtonian mechanics was a theory of everything. You would say that it isn't.
That of course does not imply that the theory of everything automatically gets you a complete description of the universe. Even in the context of a single force, it can be difficult/impossible to come up with a closed form solution for how many different objects interact subject to that force. For example, the behavior of gravity is really well understood but that doesn't mean that we can come up with straightforward, closed form solutions for the n-body problem of a bunch of stars interacting with each other's gravitational pulls in space.
http://en.wikipedia.org/wiki/Theory_of_everything