haven't read all of this, but me starting to study science (chemistry to be precise) also had implications on my spiritual growth.
first of all, science is just invention of concepts (never true to objective reality, which cannot be percieved by us), and looking which concepts match what we can see / measure best. so science is not looking for absolute truth, because this is impossible.
well the way I understood it, all is just energy in diferent states. matter is energy bound, and if you break matter, energy is released (eg dissociation of a chemical bond or radioactive decay). if you believe in the big bang theory, then before expansion of the universe started, energy was condensed into one single point, and matter only started to "condensate" as expansion went on.
so if all is essentially made up of energy, then all of the universe is the same at it's core. we are just states of energy in different places in spacetime (or something, physics and cosmology are not my strenghts

).
that's why I discarded the idea of reincarnation for myself, because if all is the same (energy), then there ultimately cannot be any difference between my soul and the others and a rock. we as human beings are energy evolved in spacetime to have consciousness and very complex behavior, and every human has their own "soul", but it only exists as long as you live, because after your death your energy will move on to some different state, and maybe ultimately be the "building block" to form another (conscious) being, maybe a cow.
I am aware that this sounds very materialistic, but to me it's not. it's the profoundness of now. I don't need "there" anymore, everything is "here".
PS: discovering Carl Sagan's Cosmos was also very influentual for me, I recommend it to anybody!