Chris,
thanks for the excellent question. In my opinion, every discrete information cane transformed into a sequence of yes/no question. But I think you are interested in the concrete example of a 4-manifold.
Has the handle (attached to the 4-ball) an index larger than 2?
Yes: it is a 3-handle
NO: Has it index 2? No: It is a 1-handle
Yes: Now I have to ask question about the attaching of the 2-handle, i.e. you have to ask about the knot. (For instance, use the braid representation of the knot and ask about the generators: Do you produce an overcrossing of the first two strands of the braid? etc.)
For the next handle start again with these questions.
The problem with the fundamental group is a little bit more puzzeling. You can do an experiment to determine the fundamental group. You can also describe this group by yes/no question but you cannot reproduce your experiment. So, the fundamental group is part of the apparatus but you cannot decide whether this group is isomorphic to the fundamental group of the second experiment.
Yes, I have a proof for the sphere bundle/graviton equivalence but it is not in good shape to present it. The main idea is the usage of a Cartan connection. Then one may ask what characterizes a (simple-connected) spin 4-manifold. Using Freedman: the Euler characteristics and the signature. Both invariants can be expressed as integrals over the Euler and Pontrjagin form, respectively.
Then using the sphere bundles and the Cartan connection one can change these invariants into the Einstein-Hilbert action (plus the cosmological constant) and into the other part of the Holst action (with Immirizi parameter).
As soon I will complete this construction you will get the paper.
Thanks for the wishes
Torsten