There seems to me a scale here, where we go from science to speculation:
1) Micro evolution: something fairly well established by science.
2) Theory of macro evolution--species can change from one to another: the prevailing theory which actively ridicules competitors...but not really a hard science. The empirical evidence lends itself to hand waving arguments both for and against. One can attempt to apply the scientific method to test this theory, but there are too many confounding factors to make such investigations definitive (as there are in psychology for instance).
3) Assertion of a single common ancestor of all species: realm of speculation. Not really testable.
4) Presumption that that single ancestor must have sprang from inorganic matter by some kind of chance (either here or on some other planet): Wholly speculative, neither testable with science, nor something which can be derived from reason.
5)Problem of where matter/energy/stuff itself came from (for which life could later spring). A compelling philosophical case for a transcendent super nature. But not something which is testable by science except on occasion and indirectly. For instance the Big Bang theory which suggests that the universe has not simply always existed--a notion which if accepted forces a reasonable man to reject naturalism.
So on the one end we have philosophy and the other end we have the scientific method as the best ways to approach the questions. In the middle is no-mans land.
Micro vs. Macro-evolution -- an argument for those unwilling to accept definitions. All evolution is micro, but it is as inexorable as erosion. You seem to think that "micro evolution" is like some editor tweaking a submission. A bit of spelling correction here, and deleting a superfluous adjective there, and voila! the work is complete!
The work is never complete. We are all too wearily aware that evolution occurs because of random events. Let us surmise that an isolated species has had more than enough minor changes to exceed any definition of micro, and yet it may or may not be a new species. What defines whether it is or not?
Generally, it is accepted that it would be a new species if it cannot successfully interbreed with other species. Then it is necessarily on its own, to prosper or perish, as fortune determines. Eventually, it may go on to parent yet more divisions, more species. Or it may simply end like the dodo.
Such isolations can occur in just a few generations, or over thousands and thousands of years. The problem is, micro just doesn't know when to stop.
"a single common ancestor" -- Well, if you think multiple origin makes more sense, you can go with that. Some forest fires have multiple points of ignition, caused by lightning strikes. And many earthquakes are preceded by "micro-quakes".
Life is pretty diverse, but not quite so diverse that some relationship seems unlikely. The discovery and analysis of DNA gave us the opportunity to see whether, and to what degree, we are all related. Not just speculation, but chemical results. And guess what? We're all related.
"that single ancestor must have sprang from inorganic matter by some kind of chance" -- Here you are entirely correct. This is neither testable nor deducible. What will we conclude if we find life existing on other worlds?
"where matter/energy/stuff itself came from" -- What good is time and space? If you had the ability to create time and space, what could you use it for? Maybe it's just an arbitrary, random event, like the dance of dust motes in sunlight.
"the Big Bang theory which suggests that the universe has not simply always existed--a notion which if accepted forces a reasonable man to reject naturalism."
The Big Bang Theory comes out of simple forensic analysis. When it was deduced that galaxies were moving apart from each other, it became a natural mental exercise to wonder what it would look like to reverse the action. Reversing the action makes it look as though there was a tremendous explosion about thirteen billion years ago.
But I cannot infer a reason that a man should reject naturalism, or even alcoholism, simply because the Universe has not always existed. Who gives a snap what was happening thirteen billion years ago?