From the perspective of the Gelfand–Naimark theorem, the heart of the reconstruction theorem is the following statement, Theorem 11.4 in Connes's paper:
Let $\mathcal{A}$ be a commutative unital complex $\ast$-algebra. Then $\mathcal{A} \cong C^\infty(X)$ for some compact oriented smooth $p$-manifold $X$ if and only there exist a faithful $\ast$-representation $A \to B(H)$ on a complex Hilbert space $H$ and a self-adjoint unbounded operator $D$ on $H$ such that $(\mathcal{A},H,D)$ is a $p$-dimensional commutative spectral triple.
Your Question 1 asks for the proof of the “only if” direction of this statement, which essentially goes as follows. Let $X$ be a compact orientable smooth manifold. Then you just pick your favourite Riemannian metric for $X$ and correspondingly form a commutative spectral triple as follows:
- if $X$ is even-dimensional, take $(C^\infty(X),L^2(X,\wedge T^\ast_{\mathbb{C}} X),d+d^\ast)$;
- if $X$ is odd-dimensional, take $(C^\infty(X),L^2(X,(\wedge T^\ast_{\mathbb{C}}X)^+),d+d^\ast)$, where $(\wedge T^\ast_{\mathbb{C}}X)^+$ is the $+1$ eigenbundle of the chirality operator on $\wedge T^\ast_{\mathbb{C}}X$.
Of course, there's some checking to do, as is indicated in Connes's account.
Now, if you combine the bare-bones reconstruction theorem with (the proof of) the “baby reconstruction theorem” in Gracia-Bondia–Varilly–Figueroa and a slight weakening of the orientability condition in the definition of commutative spectral triple, you can say even more (see Corollary 2.19 and its proof here, though the account is a bit out of date):
Let $(\mathcal{A},H,D)$ be a $p$-dimensional commutative spectral triple. Then there exists a compact oriented Riemannian $p$-manifold $X$, a Hermitian vector bundle $E \to X$, and an essentially self-adjoint Dirac-type operator $D_E$ (i.e., a first-order differential operator such that $D_E^2 = -g^{ij}\partial_i \partial_j + \text{lower order terms}$) such that $$(\mathcal{A},H,D) \cong (C^\infty(X),L^2(X,E),D_E),$$ where $\cong$ denotes unitary equivalence of spectral triples.
Conversely, if $X$ is a compact oriented Riemannian $p$-manifold, $E \to X$ is a Hermitian vector bundle, and $D_E$ is an essentially self-adjoint Dirac-type operator on $E$, then $(C^\infty(X),L^2(X,E),D_E)$ is a $p$-dimensional commutative spectral triple.
This, in particular, answers your Question 3 as restricted to commutative spectral triples. If you drop commutativity, no such classification exists. Indeed, there come to mind a couple of extremely straightforward ways to get spectral triples with algebra $C^\infty(X)$ that aren't commutative spectral triples:
- Let $D$ be an essentially self-adjoint elliptic first-order differential operator on a Hermitian vector bundle $E \to X$ that isn't Dirac-type. Then $(C^\infty(X),L^2(X,E),D)$ is a perfectly good spectral triple that, in general, satisfies all the conditions for a commutative spectral triple except orientability and the additional “strong regularity” condition—the point is that orientability and strong regularity, together, would imply that $D$ was indeed Dirac-type. A somewhat silly example is $(C^\infty(X),L^2(X,E_1 \oplus E_2),D_1 \oplus D_2)$, where $D_1$ and $D_2$ are Dirac-type operators for distinct Riemannian metrics $g_1$ and $g_2$ on $X$.
- Let $(C^\infty(X),L^2(X,E),D)$ be an honest $p$-dimensional concrete commutative spectral triple. If $M$ is some bounded self-adjoint operator on $L^2(X,E)$ that isn't a bundle endomorphism, then $(C^\infty(X),L^2(X,E),D + M)$ is a spectral triple of metric dimension $p$ that cannot possibly be a commutative spectral triple; indeed, $D$ cannot even be a differential operator. In particular, if you take to be a smoothing pseudodifferential operator (e.g., the orthogonal projection onto the kernel of $D$, if it's nonzero), then your new spectral triple should satisfy all the conditions for a commutative spectral triple except order one and orientability.
Finally, let me turn to your Question 2. Suppose you start with a concrete commutative spectral triple $(C^\infty(X),L^2(X,E),D)$ and feed it into the reconstruction theorem to get $(C^\infty(X^\prime),L^2(X^\prime,E^\prime),D^\prime)$. Then, in particular, you have an algebraic isomorphism $C^\infty(X) \cong C^\infty(X^\prime)$, which, by a theorem of Mrčun's, is necessarily given by composition by a diffeomorphism $\phi : X^\prime \to X$. Using the various axioms and the smooth Serre–Swan theorem, you can then check that the unitary $U : L^2(X,E) \cong L^2(X^\prime,E^\prime)$ is, in fact, given by a unitary isomorphism of Hermitian vector bundles $(E^\prime,X^\prime) \cong (E,X)$ covering $\phi : X^\prime \to X$, and hence, since $U^\ast D^2 U = (D^\prime)^2$, that $\phi$ was an isometry. Indeed, if you compare the Hermitian metrics on $E$ and $E^\prime$ with the inner products on the Hilbert spaces, you can even conclude that $\phi$ was orientation-preserving. Hence, if I'm not too mistaken, you can even refine the above refinement of the reconstruction theorem as follows:
Let $(\mathcal{A},H,D)$ be a $p$-commutative spectral triple. Then there exists a compact oriented Riemannian $p$-manifold $X$, a Hermitian vector bundle $E \to X$, and an essentially self-adjoint Dirac-type operator $D_E$ (i.e., a first-order differential operator such that $D_E^2 = -g^{ij}\partial_i \partial_j + \text{lower order terms}$) such that $$(\mathcal{A},H,D) \cong (C^\infty(X),L^2(X,E),D_E),$$ where $\cong$ denotes unitary equivalence of spectral triples. Morever, the data $(X,E,D_E)$ is unique up to orientation-preserving isometry together with unitary bundle isomorphism covering the isometry that intertwines Dirac-type operators.
Note, though that being or not being spin$^\mathbb{C}$ or spin is completely irrelevant to the machinery of the reconstruction theorem; the point is that you can form, for instance, the Hodge–de Rham spectral triple (i.e., the $d+d^\ast$ spectral triple) of a compact Riemannian spin$^\mathbb{C}$ manifold without choosing a spin$^\mathbb{C}$ structure. The only way this formalism can even see a spin$^\mathbb{C}$ structure is by choosing your Hermitian vector bundle to have been a spinor bundle—in light of Connes's Theorem 1.2, for an abstract $p$-dimensional commutative spectral triple $(\mathcal{A},H,D)$, this is equivalent to requiring that the representation of $\mathcal{A}^{\prime\prime}$ on $H$ have the correct spectral multiplicity $2^{\lfloor p/2 \rfloor}$, corresponding to the correct rank of a spinor bundle. In particular, if you start with a given spinor bundle, then the reconstruction theorem will necessarily spit out an isomorphic spinor bundle, so that if you do choose a spin$^\mathbb{C}$ structure by choosing a spinor bundle, then the reconstruction theorem can't change the spin$^\mathbb{C}$ structure. Again, the Hodge–de Rham spectral triple is completely agnostic about any spin$^\mathbb{C}$ structure, so that the reconstruction theorem, on its own, is completely agnostic about spin$^\mathbb{C}$ structures.