Einstein DOES explain EXACTLY how matter and energy are related.

E = mc^2.

That's all the explaining you need.

Energy and mass are NOT two separate entities, they are different aspects of the same thing. Classical physics did not recognize this equivalence. Einstein did. Your sentence

"If energy and mass are two separate entities how do they combine to form the mass/energy unit?"

is simply dead wrong. The concepts mass and energy as described in classical physics are NOT "two separate entities". Your question has no answer because it isn't even a valid question.

Photons do not accelerate or decelerate, they travel only at the speed of light. That is the definition of photon: that which travels at exactly the speed of light, no slower and no faster. It is the only thing which travels at that speed. It is a measurable physical phenomenon capable of interacting with matter and space-time and which, depending on the way it is considered, can be described as either a particle or wave phenomenon. The apparent "slowing" of light in a refractive medium is an electron emission/absorption phenomenon that takes place in atomic electron shells. It has nothing to do with photons changing speeds, although it is often helpful to think of it that way to help visualize what is happening when light is refracted. What is actually occurring is electrons jumping up and down energy states as they interact with photons, absorbing and re-emitting them. This is why different transparent media have different refractive indices and light appears to travel slower in them than in vacuo. They have different atomic structures.

This formula you keep on talking about, but which you never seem to be able to reproduce, has never been able to explain any observation or experiment, or been useful as the basis of any technology. It is just talk.

Johannes, I am not saying that Einstein can't be wrong, or incomplete, or that relativity is the last word in physics, or that it won't ultimately be replaced by something that helps us understand better; but that knowledge will come only from observation and experiment, hypothesis and testing, not from filozawfigal speculation. The universe doesn't care whether or not you agree or disagree with it. The games you are playing, trying to cast the universe in terms that seem more reasonable or more elegant to your taste, are not physics. They aren't even consistent algebra.

And you've got me curious. What is this 19th century book you keep referring to obliquely where you seem to be deriving all these insights?