At the beginning, there were no atoms, because densities were too high for atoms to exist. It was some weird quantum soup of particles.

Also, not sure where you are going with knowing the size of hydrogen atom. You can't simply pack those as tight as possible. As you pack those hydrogen atoms more and more tight, at some point protons will capture electrons, turn into neutrons (and release neutrino in the process). This is how neutron stars form. Neutron stars are about densest you can get matter before it collapses into a black hole.