This paper is a merger of a lot of complicated issues. For other readers, the paper is posted on arXiv here:
https://arxiv.org/pdf/1305.1045.pdf
Basically the problem they are addressing is that the standard model can only be described perturbatively (as a coupling constant expansion), keeping the first one or two perturbative terms. They look to turn this into a "Hamiltonian quantum theory" (a term I have not heard before, but as they define in the paper a theory which is described by operators and has a time evolution described by a quantity such as U(t,t') = \mathcal{T}exp(-i\int_{t_0}^tdt'V_I(t'))) in order to get an exact description of a SO(10) gauge theory by placing it on a finite lattice.
He also mentions a finite dimensional Hilbert space, but I assume this means they are introducing boundary conditions somewhere. The most helpful places to look are in the appendices, as this is where they show the math. It goes into the Clifford algebra of the hopping elements and how they place this chiral gauge theory on a lattice.
But to answer your first question, you need to clarify yourself. This paper combines many advanced topics, so just asking for a general reference to understand it isn't answerable. What specifically are having trouble understanding in the paper? Also, if your specific difficulty involves standard model questions, you should move over to the high energy forum. If you have questions regarding the lattice model their using and how gauge theories can be described on it, then this is the right forum.