Let me now answer your specific questions:
1. The algebra of quantions is generated, but not freely (the generators satisfy some identities). It is a unique and rigid structure, like the algebras of complex numbers, quaternions, or octonions. It is useful to view it as a number system because it replaces the complex numbers in quantum mechanical states.
2. The algebra of quantions does not require a bundle structure for its definition. But it is true that one can consider quantionic fiber bundles over a Riemannian base space. I don't know whether this will lead to new insights relevant to quantum gravitation, but I intend to look at it. I am not there yet in my systematic investigation of quantionic properties.
3. Quantions do make contact with standard quantum mechanics in a clear way. To see how, please temporarily take my word for the following two mathematical facts: (1) The algebra of quantions may be viewed as the relativistic extension of the field of complex numbers. (2) The structure of the algebra of quantions gives rise to a universal quantionic field equation in a Riemannian space (I restrict myself initially to the affine Minkowski space). This field equation contains an arbitrary mass parameter and four arbitrary vector potentials. Now, restrict the quantionic field to an infinitesimal neighborhood of the complex numbers, and apply to it the procedure that yielded the universal field equation. What you get is the standard Schroedinger equation with an arbitrary potential. The quantionic field reduces to a complex scalar function (Schroedinger's wave function). Please note (actually take my word for it, because it is not evident) that quantions arose as the unique solution to some abstract requirements that do not include the concepts of space and time. These concepts emerge from the uniqueness of the solution. Similarly, the Schroedinger equation pops up spontaneously. There is no underlying classical mechanics, energy equation, or canonical quantization. On the contrary, running the canonical quantization equations in reverse yields the concept of kinetic energy and energy conservation. This might be a way of obtaining classical mechanics (the Poisson bracket) from quantum mechanics, but I did not try. What I am currently working on is more urgent than following this tangential idea.
4. The Clifford algebra of Dirac matrices and the algebra of quantions are related by way of the Von Neuman algebra (of upper-case gamma matrices). They correspond to two different selections of basis vectors in that algebra. In the Dirac case, the 16 non-Hermitian basis elements form the well-known lattice {scalar(1), vector(4), bivector(6), pseudovector(4), pseudoscalar(1)}. In the quantionic case, the 16 basis elements are Hermitian and are generated by four elements, let's say {A,B, X,Y}, whose squares are I (the unit matrix) and are such that {A,B} = {X,Y} = [A,X] = [A,Y] = [B,X] = [B,Y] = 0, where {*,*} is the anti-commutator and [*,*] the commutator. Please note that these relations have not been cleverly constructed in order to get some interesting consequences; they are themselves consequences of the algebra of quantions, whose origin is conceptual.
I hope this post will be helpful. I would gladly send you a copy of my 2007 book if you tell me where. I live in Manhattan.
Best regards,
Emile.