Hi Martillo,
What I do not understand, is that you don't start to read. Several experts here have told you, that electron configuration in atoms and molecules, and chemical bonds, are thoroughly understood, and already belong to established science. Of course, there are still problems enough, but many (most?) of them are practical: even if we have the basic theories, the calculations become next to impossible when many particles are involved, and therefore approximations or experiments are needed. (just imagine: there is still no general analytical solution for the 3-particle problem , i.e. 3 particles that move under simple Newtonian gravity! How more difficult is it when you want to describe multiple particle problems for atomar conditions!)
The problem you have seems to me that what you understand about these topics so far, does not fit the concepts you use to approach atomar and molecular processes and configurations. I can only say: believe the experts here, and the established science, that there is no problem. There simply is no need for a new basic theory, so don't spill your time on it.
Use your time to get into the present scientific understanding. Read about quantum theory, quantum electrodynamics, and chemical bonding. Try to find the books that fit to your present understanding, and bring you to a higher level of insight about these topics. I am sure that some of the participants in this thread will help you to find the right books (or maybe even good web pages). I assure you, great new vistas will be opened in your mind.
Let us know, if you need any help to find the right texts for you.
Cheers,
Eise