What got me thinking the most was my reading on 'antiparticles' - 'stable' particles (any particle in the atomic scale) that operate on a negative charge. In a 'normal' (positively-charged) atom, the positively-charged nucleus (consisting of neutrally-charged neutrons and positively-charged protons) attracts the negatively-charged electron, yet the energy of the electron is not enough to overcome the nucleus' 'binding force' and is repelled by it. The same laws hold true if an atom's nucleus and electron(s) are both negatively-charged. Yet when a particle and its polar-twin antiparticle (say, a hydrogen atom and a 'anti-hydrogen' atom) enter into contact, they annihilate each other, and the same would happen if a positron (positively-charged electron) and electron converge; I am persuaded that whatever is 'left over' from these collisions would be 'neutral state' matter.
Whatever this 'neutral state matter' is, it is capable of accepting a charge, but the conditions in which this could happen would have to be extreme. I imagine an effect almost like water skipping off a duck's back; a ducks's feathers have waterproofing enough to resist absorbing the water propelled on them under 'natural' conditions, but were the water propelled with enough energy (and/or volume), the feathers would be obliged to absorb moisture. This action could explain the behaviour of rays (energy) through a seeming void: if the energy is not travelling with a force/speed enough to affect the 'base state' matter, it will simply skip across it. This may even define the speed of light; any energy above this level is absorbed by the 'base matter', thus becoming invisible to us - or would it create a new perfectly-visible particle?
This model still makes sense when applied to particles as small as quarks. Once a 'base matter' particle becomes charged, it gains mass; it is still 'attracted' back to its 'neutral' state, but is impeded from doing so by its charge. How the newly-formed particle behaves with its neighbouring particles depends on how it is charged: according to today's model, an 'up' quark has a 2/3 charge and a 2.4 MeV mass, and a 'down' quark has a -1/3 charge and twice the mass, and these, once created, would 'clump' into 'stable state' Hadrons (Protons and Neutrons).
I wouldn't be at all surprised if quarks and electrons, if they are not one and the same, are at least in the same family: it would make sense if, at the beginning of the universe, the quark-energy soup combined to form all the Hadrons (Protons and Neutrons) it could, and electrons are simply 'free' negatively-charged quarks 'left over' from this grouping/inter-annihilation: these particles would be attracted to the already-formed Protons by their negative charge, but would lack the energy needed to affect the Proton's already-stable state ('binding energy'), thus gravitate around them.
Atomic construction from then on was consequential, through methods already well-known to us.