I don't have to refute any of that to support the notion that adding "under God" to the Pledge of Allegiance violates my interpretation of the Establisment Clause (I say "my interpretation" because all opinions on the issue are interpretations of one form or another). Just because someone who helped draft the Constitution then goes out and does something that in my opinion would violate part of the Constitution, doesn't mean on it's face that what he did was constitutional.
Throughout our history men in power have done things that are unconstitutional. Are we now to say that those things were constitutional because they were done? Just because something is done by the President or by an act of Congress does not by default make it Constitutional. The Lincoln haters would certainly agree on that point.
That said, here's the refutation you requested.
Points 1 and 2 have no bearing on the Establishment Clause whatsoever and therefore are meaningless. The Establisment Clause specifically targets Congress not individuals. These points are Strawmen.
I need more context on Point 3. When was this law supported? Before or after the Constitution was written? On it's face I would say though this is also a meaningless point because The Establishment Clause does not pertain to State Legistlatures (although it has been applied to state legislatures which I think is a mistake).
Point 4 is meaningless. This issue hasn't come up before a Court of Law so no decision has been made to either remove or keep the religious symbols in the Judiciary. But I would say that this does not violate the Establishment Clause because the Clause does not pertain to the Judiciary and as far as I know Congress has passed no law mandating those things there.
Point 5 is meaningless. Or would you argue that Brown vs. Board of Education was a mistake because Plessy vs. Fergeson had been the established law for decades? Like it or not both Conservatives and Liberals change their views over time. Nobody today would support Plessy.
Point 6 is meaningless. Regardless of what the Northwest Ordinance currently says (if the law is still valid and I'll take your word for it if it is) nobody has standing to challenge it on the Establishment Clause because we haven't admitted a new State in decades and in all likelihood never will again. You have to keep in mind that some of these things that technically violate the Establishment Clause have to be challenged before they can be ruled on their Constitutionality. I doubt anyone's challenged it. But that doesn't make it Constitutional.
notice that this one indicates a view of the Establishment clause that is of a modern conservative, that it strictly refers to a legal establishment of a faith
Fair enough. Here's something for you to chew on then. If there is no faith involved in the phrase "Under God", why are so many people complaining about how this decision is an attack on Religion? If the Pledge is so religion neutral and God is just a being, why all the Religious rhetoric then? It seems to me that an awful lot of people are complainging on religious grounds to a phrase they claim has no religious significance. It seems to me they are undermining the very claims they seek to make.
Also if you want to include people's commments about the laws they write as basis for what they wanted to attain, then Eisenhower's comments alone make the modified pledge a violation of The Establishment Clause.
Please keep this in mind. I thought this was a stupid decision. It's nitpicking. It's not worth the struggle. The dissenting judge was correct in that regard. It only succeeds in riling people and diverting attention from more pressing matters. The Pledge in its current form doesn't bother me and I wouldn't seek to take the Government to court over it or a bunch of other Establishment Clause cases that we've seen over the years (particularly X-mas scenes). But I think that technically it was a Constitutionally correct decision.