Putting everything together, I have argued—using plausibility arguments, not strictly deductive proofs—that it is reasonable to believe in a metaphysically ultimate being, and that given the reality of Ethics or Consciousness, it is probable that it is more like a mind than like a set of equations. More specifically, my arguments pointed to just one eternal God, existing necessarily, who is all-powerful, all-knowing, and good, who is the source of all other things, yet is distinct from them, and who appreciates mathematical beauty, conscious life, and ethical behavior.
Of course there are a lot of mysteries left in this view. Even though God is supposed to be the explanation of all other things, we cannot predict, from this information alone, exactly which laws of physics God would select, nor whether he would intervene in the Universe thus created in other ways. Not sharing the divine knowledge about what is best, we have to make additional stipulations about the world he has created, adding to the complexity of any specific Theistic worldview.
But then again, Naturalism by itself cannot tell us either (apart from experiment) which specific laws of nature to expect. All views contain a certain amount of irreducible mystery. The difference is that Naturalism hides or denies the mysteries, and pretends to solve problems that it cannot possibly really solve, while Theism puts them up-front and center and does the best it can to fit them into a consistent picture of the world.
It does not matter so much whether you are convinced that my conclusions have to be right. Maybe there were several places in the argument where I selected one of two paths, but you think it was a toss-up, or that the other way was somewhat more plausible. That's part of the hazards of armchair reasoning. Personally I am primarily concerned with the arguments for Theism as a prelude to Christianity, which is founded on the Resurrection of Christ and the testimony of God's Spirit, not philosophical discourse. But plausibility arguments still have their place. If you are thirsting after goodness and beauty and meaning, and if you learn that there could well be a fountain capable of slaking that thirst, shouldn't this increase your incentive to search for it?
A purely intellectual philosophy can only get you so far. Actual religion involves opening yourself up to the divine being, over a continued period of time, allowing God to get hold of you. Any approach must be by his initiative rather than yours, but your attitude can determine whether or not you are receptive to his advances. Without this, philosophy is sterile. If it advances only to savoir, conceptual knowledge, it might as well have remained atheistic. All of these philosophical arguments are only there to help you make further steps, to connaître or knowledge by acquaintance. Arguing for the existence of the Good is one thing; tasting the reality of the Holy is another.
When that happens, the purely intellectual arguments—and the doubts which are a necessary corollary of any honest attempt to evaluate them—can be kicked aside like a ladder that has served its purpose, and replaced with something far better.