I totally disagree that the citations you just posted support the assertion that Story was talking about modifications to the Constitution that would constrain the states. The very mention of bills of rights in various state constitutions convinces me that Story recognized that the protections of the various states were not all identical. I agree that the various commentators all believed that many of these rights were unalienable and therefor applied to the states INDEPENDENTLY of the U.S. Constitution and INDEPENDENTLY of any explicit statement anywhere. But I don't read into the comments you have provided that they believed that a modification to the U.S. Constitution amounted to a modification to every state constitution.
Section 10 of Article I of the Constitution contains three clauses that explicitly bind the states. But such things as the prohibition against ex post facto laws does not appear there and does not contain language that would make me believe that such a prohibition applied to the states by virtue of appearing in the U.S. Constitution.
Did every state, at the time of the ratification of the U.S. Constitution bar ex post facto laws? Is there any state which didn't bar them which was later found to be in noncompliance with a mandate from the U.S. Constitution which bound them to prohibit such laws?
Then you are obviously reading something with a different perspective than mine. To me, in light of the clear language of the text of the legislation that passed the BoR and Art 6 Para 2, it cannot mean anything else.
Is there any state which didn't bar them which was later found to be in noncompliance with a mandate from the U.S. Constitution...
There have been a number of State laws the have passed the State legislatures and found to be in violation of the US Constitution. FindLaw is probably full of them...