You have very interesting and profound questions. I'll try to answer them one by one.
1. The matter anti-matter asymmetry is a well known and little understood problem. Many prominent physicists have pondered it. Andrei Sakharov studied it and described the necessary conditions for the asymmetry to exist, shttp://en.wikipedia.org/wiki/Baryogenesis
. There might be separate areas in the universe that are anti-matter dominated. They could even out the asymmetry. However in our local region of the universe observations have revealed none, since the boundary between matter and anti-matter should be prolific regions of annihilation radiation that we see no evidence of.
2. The apparent randomness in observed matter density fluctuations: stars, galaxies, galactic clusters etc., arise from the quantum mechanical fluctuations soon after the original big bang. These tiny perturbations then grow into large scale matter density fluctuations. Global mass distribution fluctuations tell us a great deal about the make-up of the early universe. For example the mass of the elusive neutrino has been constrained by looking at large scale density fluctuations. See: http://iopscience.iop.org/1475-7516/2006/06/019/pdf/jcap6_06_019.pdf
3. After the big-bang the growth and accumulation of nuclei, atoms, molecules, etc. is determined by the strength of the interactions as well as temperature of the constituents. For example the elemental nuclei, hydrogen, deuterium, helium... are bound by the strong nuclear force. Atoms, like hydrogen etc., are bound by weaker electrical forces, so have to wait around for a bit for the universe to expand a bit and cool down.
(published on 08/25/10)