First of all, let us address the argument from the answer by Andrew, that one “cannot compare the velocities of two galaxies separated by 100 Mpc”. While, for a general spacetime statements like this can have merit, FRW spatially flat cosmology is an interesting example of a curved spacetime, that is well described by Newtonian gravitation globally, including on scales exceeding the Hubble radius (provided, of course, that gravitational effects from relativistic sources, such as cosmological constant, radiation etc. are recast in the Newtonian language). Homogeneity of FRW provides us with a natural splitting of spacetime into “slices” of constant cosmic time, which are basically flat Euclidean 3D spaces. So if there are vectors defined at different points of space at the same time, these vectors could be parallel transported to a common tangent space and thus compared. In practical terms, this means that for large scale numerical N-body simulations of cosmological structure formation we can use Newtonian gravity over cosmological distance instead of Einstein equations.
Now, as the universe expands according to FRW metric, will the distance between the two galaxies increase with time as $d=>a(t)d$?
No. The evolution of the distance between the galaxies could be determined form the second Friedmann equation:
$$
\ddot{d} = \left(-\frac{4 \pi G \rho_\text{m}}{3} + \frac{\Lambda c^2}{3}\right) d . $$
This is the equation for relative acceleration for particles in the Hubble flow but it would continue to be valid also for particles not moving with it, provided that the relative velocities remain small compared to $c$, otherwise one has to include relativistic corrections to the acceleration.
Note, that this is a 2-nd order ODE and we need to specify not only the initial separation $d_0$ but also the initial velocity, which, as specified in the question, is zero $\dot{d}(0)=0$. In our universe the expression in parenthesis is positive at present, so the distance would be increasing but slowly at first, and only after sufficiently long time (about Hubble time) the growth of distance could be approximated as $d=C a(t)$ (note, that $C\ne d_0$). Also note, that if we imagine the universe without cosmological constant (pure dust cosmology) the acceleration $\ddot{d}$ would be negative, and the distance between these two galaxies would be decreasing until they collide (or approximation of uniform matter distribution stops working).
If no, then is the expansion of universe really an expansion of space, or is it just that all matter are moving away from each other due to some initial explosion, like the big bang?
This is not an either/or situation. Space is expanding and thus bits of matter are moving away from each other. But unlike explosion there is no external reference which allows us to define center or absolute state of rest.
Will the light emitted by one galaxy be redshifted to the other galaxy, as there is no relative velocity in the physical distance space, and hence no doppler effect?
If the light is emitted from the first galaxy when both are static relative to each other, by the time it reaches the second galaxy, this galaxy would be moving, so the light would appear redshifted to the observers of the second galaxy, but this redshift would be smaller than that from the Hubble law.
If yes, then isn't it a violation of conservation of momentum? Two bodies initially with zero relative velocity and zero interaction suddenly starts to move away from each other?
This is no more violation of conservation of momentum than an apple initially at rest relative to Earth and starting falling toward it. Relative acceleration of those two galaxies is determined by the cosmological constant and by the density of matter between them. We can apply the shell theorem of Newtonian gravity and ignore the influence of anything outside the sphere, then the total momentum inside the sphere is conserved.
… then what is the nature of the force/energy which is supplying the potential well to "glue" particles to the expanding comoving coordinate system?
Particles are not “glued” to the comoving system, in Newtonian language they are moving only under the force of gravity which has two components: gravitational attraction toward matter and gravitational repulsion from cosmological constant.