Yes, it’s certainly true that the idea of a single sovereign national legislature was rejected at the founding. The Continental Congress acted as a kind of clearinghouse of the states’ policies/diplomatic arena, not as a sovereign legislature; the Confederation Congress had narrowly constrained powers; and the US Constitution is a federal constitution, not a sovereign body. Thus, this didn’t shift between the Revolution and ratification.
Yes, Wilson acted after ratification in some senses as if the US Government were sovereign in the old British sense.
Wood’s account of Adams’ thought on this score is generally accepted among historians and political scientists. I’m currently reviewing a new Adams biography for The American Conservative in which the author says Adams had no theory of federalism–which seems about right.
Wood does miss that in Virginia, at least, Federalists said during the ratification contest that states would have the option of secession if they ratified.