Aha, I'm glad to have provided something you enjoyed reading so much, TFP, and that you find so much to agree with.
In what way was the mention of animal sacrifice and the other ritual practices an error, though? If there is not supposed to be any detectable effect of such practices, why do any religions bother with them? And if there were more errors you caught, what were they?
When you say he jumped into philosophical traps, do you mean with enthusiasm, as in, "He jumped into his new career," or do you mean his own arguments fall to the logical criticisms he applied to religious arguments? As far as the disparities between competing religious truth claims, he says he thinks it calls into doubt the truth of each. If you, as he almost certainly does, consider those disparate truths in light of the lack of convincing empirical evidence proffered in defense of them, doubt is entirely reasonable. Also, what were the issues with his defense of naturalism, and do you mean philosophical or methodological naturalism? Barbara Forrest on naturalism is, in my experience, good philosophy.
To tie up, correct me if I am mistaken: you largely agree with Coyne's conclusion that the problem facing scientific literacy in the US is high religiosity, itself an effect of our social dysfunction? And could you describe to me where he fails to operate within the definition of religion he gave at the top of page 2655? Anyway, I am still curious about your estimate of the fundamental problem.