1. Nothing is vibrating. The Michelson-Morley experiment proved that. If the "fabric of space" was vibrating, we would be able to tell by noting changes in the speed of light due to our motion, and the motion of the emitting source, through it. With sound, or water waves, their speed changes as the source or observer moves through the air or ocean. This doesn't happen with light waves. Light is not a wave. It does exhibit some characteristics that waves have. The speed of light emitted by a moving source is not affected. However, its frequency, is.

2. Who knows? That is just a fact we have observed. It doesn't need a reason, it just is.

By the way, the energy of a photon can be calculated if you know its frequency: Energy = h x frequency, where h is Planck's constant, a number which relates Joules (the unit of energy) to Hertz (the unit of frequency). One Hertz = 1 vibration per second. h = 6.62606957 × 10^-34 m2 kg / s. The units of h, meters, kilograms and seconds, ensure that the resulting energy is expressed in metric units of Joules.

3. Energy is the ability to reverse entropy. Or to put it another way, the ability to do work. It is not always a "thing", it often is a relationship between things. For example, an ant riding on a speeding bullet has no way of telling he is moving. He can perform no experiment that shows he is moving or has energy. Only if he sees stationary objects around him, (or runs into an object!), can he tell he has "kinetic" energy. Since everything is moving relative to everything else (there is no inertial reference frame) there is no intrinsic kinetic energy in any moving object.

It must all be referenced to objects you can observe or otherwise come in contact with. Unlike kinetic energy of motion, other types of energy (chemical, radiative, electrical) are intrinsic to the object, not its relation to its surroundings. But energies can be transformed from one form to another. So our flying ant has no way of knowing he has kinetic energy, but that kinetic energy was created by the chemical reaction that propelled the bullet. And it is transformed into heat, sound, and other forms when the bullet strikes a target.

4.That which energy acts on. Think of it as a noun, the object of a sentence. Energy is the verb.

5. The energy in a wave form is expressed by the motion of matter affected by it. If two wave trains cross and interfere, matter placed at the nodes where the waves cancel out (peak to trough) is unaffected. Matter located where the peaks and troughs line up (peak to peak, trough to trough)is affected profoundly. A ship in a seaway, subject to multiple wave trains, will see brief periods of flat water and deep troughs and rogue waves, depending on whether the waves at that spot reinforce or interfere.

Your questions are good ones, but they also betray that, like our ancestors, you are being misled by your preconceptions of cause and affect. You can't think in terms of what causes phenomena to occur. You must simply observe the phenomena and note their characteristics and results. The universe just is, there is no reason or purpose to it. Like shit, it just happens.

What happens, or doesn't, appears to be regulated by specific rules (the Laws of Nature)but not because they are caused by anything, Its just another way of saying there is a reason for everything, but a purpose to nothing.