TheAtomicBun: taking your points in turn:
Yes, we could easily quantify the gravitational effect of an atom. It's simply a function of it's mass, which we know how to measure.
What we cannot yet do is describe gravity using the theory of quantum mechanics. These explains the forces of nature in terms of the exchange of particles, however the particles themselves behave in ways that cannot be described using classical theories. Notably, the particles can also behave as waves and it is this wave-particle duality that underlies quantum mechanics.
The classic example is light. Light behaves as a wave - it has a frequency and polarisation and other qualities of waves. However it sometimes also behaves as a particle (which we call a photon) depending on how you observe it.
This wave-particle duality, and the effects it has is very well explained by Quantum Mechanics, to the extent that 3 of the 4 forces of nature (the electric force, the weak nuclear force, and the strong nuclear force) can all be explained by this theory.
The stand-out is gravity. We have an excellent classical theory of gravity, general relativity. However, we have not yet formulated a quantum theory of gravity that demonstrated the effects predicted by general relativity. We've also never seen the theoretical force carrier particle, the graviton.
Physicists really don't like anomalies like this. It smacks of broken symmetries and lots of other things that make them itchy.
Regarding the missing mass, it is suggested that the universe is filled with a dark matter that we cannot see by normal means but can infer the presence of by it's gravitation effect on galaxies. The dark matter would have to be formed of WIMPs (weakly interacting massive particles). We're currently trying to detect these, but as they only very weakly interact with normal matter it's proving a bit tricky.
The "God Particle" that you refer to is the Higgs' Boson. It's a particle, the presence of which is predicted by the standard model, which has the special property of conferring mass. From mass, we get gravity, which is why it is considered pretty important. We haven't found one yet, but we're looking!