May I simply note the complete absence of argument in your response. Yes, God could have eliminated the pretext that was used to justify religious war by Christians. And what other massacres might have happened in a world where those pretexts were missing? I don't know, and neither do you. This is one side of the argument from evil.
Christians who have had the power to use force to promote their doctrines have done so, with bad consequences. Christians, however, are the ones who eventually learned their lesson and separated church and state. If atheists become sufficiently powerful politically to force their nonbelief on others, will they do so? The only examples we have of governments where atheists had sufficient power to impose atheism do not give us much cause for optimism. Oh, maybe there won't be burnings at the stake. Maybe just insane asylums for the incurably religious. After all, they were brainwashed to begin with, so what could possibly be wrong with brainwashing them into being right-thinking folks? I don't think atheists have cause for self-righteousness about such things. It is human nature that leads us to kill one another, and we will use anything we care deeply about as a pretext. Including atheism.
Your arguments raise serious questions for Christians. But the rhetorical noise level in what you write doesn't help us discuss those questions.
I mean, I do not have a specific answer for why God didn't make certain issues that became points of contention in the wars of religion clearer. And for that I am to abandon my beliefs and accept what? A world where the very pains that form the basis for the problem of evil are difficult to explain? A world where there are no objective moral values, and therefore the value of tolerating people you think caught in a delusion is also not objective? A world which is at its core irrational, but produced rational beings smart enough to do the math and science necessary to put a man on the moon? A world where a great religion grows which, all told, does more good than any other movement in the history of mankind, (and I do believe this, in spite of all the problems), but which is based, in the last analysis, on hallucination and legendary distortion? A world where those who inflict unjust suffering get the same fate as those who suffer it? A world where getting all of this right just puts you in the same kind of grave as those who fell into the great Christian delusion? A world that is, in the last analysis, completely without hope?
I alluded to the complete lack of argument in your response. As passionate as you are about your unbelief, your noisy rhetoric will increasingly play only in the echo chamber of convinced atheists, the mutual admiration society you call Debunking Christianity. The questions you ask are good ones, but you don't support your work by fostering real dialogue, the kind of dialogue that goes on every day at Dangerous Idea. People on the other side who try to post and generate real discussion on your site are ridiculed and shouted down. Even atheists who question the way you go about defending your views are banned. Your constant self-promotion is tiresome, as is your incessant repetition of The Emperor's New Clothes. (I'm partial to Danny Kaye's version, myself). You tell people they are ignorant if they haven't read this or that book of yours, when your ideas are all out there for everyone to see on your website.
You think you understand Christians perfectly because you were once one. Sorry, but understanding positions you disagree with takes constant effort. Atheism, all too often, is defended with a large dose of intellectual pretentiousness, with ad hominems and proof surrogates where the argument is supposed to be.
You think that you are suddenly liberated from confirmation bias and sociological pressure by deconverting. Sorry, but it doesn't work that way. People play follow the leader in the atheist community, too, as is evidenced by the popularity of the Jesus Myth.
It is interesting how much ideological passion today's atheists have. I think I have seen it somewhere before. Oh, now I remember. At meetings of Campus Crusade for Christ.