You (and Clifford) are both making very strong and detailed arguments to back up what should be obvious to everyone: saying it is so does not make it so. However I think you are approaching this argument with the thought in the back of you head: "God does not exist, therefore dedicating your life to the study of God gives you no authority".

So dare I say it, the implicit attack on organised religion and the clergy boils down to the question of wether God exists or not, which, let's face it, we're probably tired of arguing about in the Backroom.
I know I approach it with the assumption that God doesn't exist. But god is just one of many things that we don't have grounds to believe. If I study engineering for years, I can eventually be in a position to verify whether or not the Engineer is correct in his claim. If I study religion and the bible for years, I will not be in a position to verify whether or not God exists.

The fact that an Engineer studies Engineering and a clergyman studies God does not give one more authority than the other in their given field, unless you begin by saying that the study of God is invalid.
Ah, but I am denying that morality is in the field of religion. So the given field of a clergyman is simply whichever religion he is involved in, and he may certainly be an expert on Christianity. That does not make him a moral expert. You wouldn't go to an Engineer when you needed a physics authority, would you? This is in addition to the verifiability point. It is possible for a clergyman to be a moral expert of course.

At the end of the day, it makes very little practical difference. Most theists believe in a benevolant God who wants the best for humanity. Most people believe that what is 'right' is what is 'best' for 'society'. We (both atheist and theist) can certainly apply scientific methodology in exploring (and modelling/codifying?) what this means.
I agree that they can, but there is a trend of believing that they don't need to.