Hi all,
As an introduction I got my Master's years ago in physics - specifically quantum physics. I have been around creation/evolution debates for some time and have gotten to the point where I think involvement is just counter-productive. I do, however, still enjoy answering specific questions regarding in physics and like to clear up a few misconceptions that I see over and over again. So here goes:
"Do all the things known in quantum physics and theory really make full sense all the time?"
Actually, very little of it makes "sense" but neither does most of modern physics. It doesn't really make "sense" that time slows down as you go faster and space can bend - but we can test both these ideas over and over again and show that they are in fact "true" (not absolutely true, but so experimentally verified that they are considered facts).
The problem is that people often look only at the implications of the juicer ideas of quantum mechanics and, due to the immense time commitment and specific knowledge required, fail to learn the logic and the progression that led to those ideas. The best I can do here is recommend some laymen focused texts on the subject that would do a far better job of explaining things than I would ever.
"When an electron that orbits around the nucleus of an atom gains energy or losses energy it instantaneously jumps orbits to the next upper or lower orbit around the atom without passing the inbetween distance. How is this achieved?"
This is really assuming a very out-dated model of the atom - the early Bohrian model. This model that many learn in their early physics classes shows a nucleus with electrons orbitting around it in specific places and specific orbits similar to the Solar System. Unfortunately, this simplistic model is completely wrong - electrons do not have specific orbits that they are confined to nor do they even have specific locations. An electron in any given atom can literally be anywhere in the Universe at any given moment, but is probabilistically contained to a fuzzy cloud around the atom.
The real question is how an electron can jump from one energy level instantly without ever being at an energy level between. This is the fundamental idea of quantum mechanics - that energy (and indeed space and time) is "quantized" into discreet lumps that are not infinitely divisable. This means that at the very small levels, something doesn't gain energy steadily - it gains energy in instant jumps. If one goes from 1 quantum of energy to 2 quanta - one doesn't go between 1 and 2 (i.e. it is never 1.5 or 1.2 or 1.8), it is either one or two.
Now that may seem fantastic, but it is literally the most predictively accurate scientific theory in the history of science (may sound incredible, but it is actually true - quantum electrodynamics and QFT have been verified to 15 significant figures).
"How can a photon be considered a wave and a particle at the same time?"
Because they seem to act like both. In actuality, physicists don't really consider light a wave at all anymore and have mostly discarded wave particle duality, but it is still a seful explanation in some ways. The problem is particles are not really just little balls - that is too simplistic to explain their behavior. Nor are they waves. These are just macro-scale analogs that we use to explain them and even think about them, but they are not entirely accurate.
"Is the basic constitution of matter and reality surreal in that it exists yet in the same way it don't exist but appears too?"
Well, depends upon what you mean by "exists." The Standard Model of Particle Physics describes the basic fundamental particles (quarks and leptons) are volumeless point particles. Do they "exist?" They certainly can have verifiable effects - but do they themselves "exist?" That is best a question for philosophers.
"an electron is a detectable particle made up of quarks held together by gluons."
As someone else mentioned - this is actually wrong. According to the Standard Model, electrons are not made up of quarks and gluons, but actually is a lepton - another elementary particle. You have confused electrons with much more massive hadrons (protons, neutrons, etc) which are composed of various quarks held together by gluons.
Cheers
Quantum physics doesn't make sense by our "common sense". All the phenomena you list really happen. They have been tested time and again, if for no other reason than the scientists involved were no more willing to put aside their common sense than you are. Einstein wrecked his career by refusing to accept quantum indeterminancy.
