About states, observables and the wave functional interpretation in QFT with gauge fields First of all, I'm a mathematician, so forgive me for my possible trivial mistakes and poor knowledge of physics.
In a QFT, we just start with a field (scalar, vectorial, spinorial, gauge etc), so I would like to know what are the observables and the states in this context.
In QFT, the general approach would be by using the Fock space (for the free field case, since I don't really know if this would be true for the interacting one) and getting down, by using the particles associated to the operators $a$ and $a^{\dagger}$, to QM particles (I don't really know if this is true, because the number of particles is not constant and depends on the observer) or by using the wave functional interpretation (a functional on the space of field configurations satisfying Schrödinger equation), though I've heard that this functional is not Lorentz covariant (by the way, any proof?). However, according to this article (David John Baker, Against Field Interpretations of Quantum Field Theory, http://core.ac.uk/download/pdf/11921990.pdf) the wave functional interpretation is equivalent to the Fock space, so, in any case, this interpretation is not physically reasonable.
In AQFT, in contrast, the operators are already given (so we already have the observables). Furthermore, if the Lorentzian manifold is globally hyperbolic, a Cauchy hyper surface would be a possible interpretation for a state.
In other aspect, are the quantized fields of a given QFT really observables in the sense that they measure?
Now, adding gauge fields, everything will be groupoid valued and observables would be defined on quotients by the gauge group. In this context, I haven't really seen anything written about states and I have no idea on how the Fock space would be. The naive approach would be to consider the wave functional interpretation with domain in a groupoid.
Furthermore, if we restrict ourselves to TQFT, CFT or other specific class of field theories, would all this problem be solved?
 A: The algebraic approach gives the better idea of what the states and observables of a quantum theory are, and this holds in infinite dimensional systems as well.
In the modern mathematical terminology, observables of quantum mechanics are the elements of a topological $*$-algebra, and states are objects of its topological dual that are positive and have norm one. The most usual case is to take the $*$-algebra to be a $C^*$ or $W^*$ (von Neumann) algebra; however with such choice unbounded operators are not, strictly speaking, observables (but they can be "affiliated" to the algebra if their spectral projections are in the algebra). The advantage of this abstract approach is that, by the GNS construction, one can immediately associate an Hilbert space to the given $*$-algebra (and a particular state), where the elements of the algebra act as linear operators, and the given state as the average w.r.t. a specific Hilbert space vector.
In usual physical terms, only self-adjoint operators are considered to be observables, for an observable should have real spectrum (and could be associated to a strongly continuous group of unitary operators). The quantum field is, usually, considered to be an observable in a QFT (it is self-adjoint but unbounded, so often it would be affiliated to the $W^*$ algebra generated by its family of exponentials, the Weyl operators); and it is perfectly possible, theoretically, to measure its average value on states (to do it really in experiments, that is all another problem).
Quantum field theories are almost always represented in Fock spaces. However, since the Heisenberg group associated with an infinite dimensional symplectic space is not locally compact, the Stone-von Neumann theorem does not hold and there are infinitely many irreducible inequivalent representations of the Weyl relations, the Fock space being only one of them. To complicate things more, the Haag's theorem states that, roughly speaking, the free and interacting Fock representations are unitarily inequivalent (but that is a problem mostly for scattering theory, not at a fundamental level).
The "wave functional interpretation" (never heard this terminology) is just the functorial nature of the second quantization procedure that can associate to each Hilbert space the corresponding Fock space. This is due to Segal and you may also consult Nelson. The idea is that to each Hilbert space $\mathscr{H}$ one can associate a Gaussian probability space $(\Omega,\mu)$ such that the Fock space $\Gamma(\mathscr{H})$ is unitarily equivalent to $L^2(\Omega,\mu)$, and the map between $\mathscr{H}$ and $\Gamma(\mathscr{H})$($L^2(\Omega,\mu)$) is a functor in the category of Hilbert spaces with self-adjoint and unitary maps as morphisms. The $L^2(\Omega,\mu)$ point of view becomes very natural if one is interested to study QFTs by means of the stochastic integral approach (Feynman-Kac formulas) in euclidean time.
