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Hello. I commend what you have written and the depth of thought that has gone into it, but i feel that there are some things you may have missed, that i will put forward for consideration. i have realised this was posted 10 years ago and you are probably not even on this site anymore, but i want to write it anyway!
I see Objectivist thought disagreeing with Religion (and this is my thinking) because it is not a personal moral code they are taking on; but that of a collective, so overall religion has no place for individualism and restricts, in some ways, rational thought in the place of obsequious belief (this is further backed up by Orwell in 1984, jus’ sayin’).
To address your second point, i think you have a different understanding of good and evil. You pose them to be contradictory of one another, when in fact they could only be classed as a contradiction when applied to the same situation, instead they are able to exist at the same time, but not in the same situation. You are right that Rand shows she does believe for evil to exist and i think that evil can exist, because as Rand puts in the book, the evil comes from someone who defies themselves and their own values of life and existence; that is the evil of man. The whole point of her book is to show the stupidness of man defeating their species in order of some values that is not their own. They, she believes are capable to do it through (as D’anconia puts it) through the only evil thought, not thinking.
The last reference to the soul is one that can be explained with some knowledge on Greek thoughts of the soul (Aristotle is the one major influence in rand’s life, she says). A way of seeing the soul by this line of thought is through reason, a belief was held by some that reason was the proof of the soul and part of what made it up. So by Aristotelian standards, the soul is not devoid of reason but infact the best, most humanistic part of it is made up by the capacity of reason.
I hope you read this :)