"It appears that the court is subject to the limitations imposed by the Congress. That seems to be in direct contradiction with the rest of the discussion in #78 and #81. I would be interested in your views on this?"
I have many thoughts on this.
The foremost is to pull back and have some perspective on 1788, on the author of the two articles of the Federalist you cited (Alexander Hamilton), and on the question of authority.
In 1788, when the grand debate over the new Constitution was taking place, America was striking out into the unknown. The new government was just that: new. There was no historical model for a large representative republic. Nobody knew how it would really work, so the Federalist papers, and the Anti-Federalist papers, are all speculations about how things would work, or were intended to work.
When one speaks of intent, it is always difficult to assign "intent" to a decision made by an assembly. A case in point is the difference between Alexander Hamilton, who was one of three New York representatives at the Constitutional convention, and his fellow representatives. They were sent by Governor Clinton, and they opposed the project. So, what was "New York's intent" at the convention? Was it Hamilton's? Or was it the majority of the delegation, who opposed the new Constitution project? Hamilton himself envisioned a strong monarchic system, and did not particularly like the structure agreed upon. He thought it was too weak. Madison didn't love the structure either, but considered it the best to be had. It is probably fair to say that NOBODY at the Constitutional convention was fully satisfied with the product, thinking the new government too strong or too weak. The Constitution is a political compromise document, wrought through the usual process of sausage making that is legislation.
There is a tendency to lionize the Founders as practically superior beings with supreme insight into the workings og government and a clearer vision of the future than any who came before or after. But this is simply untrue.
Nowhere is that made clearer than in the parts of the Federalist where Madison extols the virtue of the new Constitution because it will prevent the rise of factional parties which have plagued all other republics. But the end of Washington's term, factional partisanship had already become so ferocious that he sternly warned against it, utterly in vain, in his farewell address. The Founders of the Constitution did not INTEND for there to be any political parties at all. And yet within four years of the setting up of government, the very factionalism that they had piously intoned against with flowerly language in the federalist was raging in the land.
They were not prescient. And they didn't speak with one voice. Indeed, in Jefferson's government Madison took positions that were diametrically opposed to some of what he wrote in The Federalist a little over a decade before.
The government developed and operated in ways that were surprising to all parties, even in their lifetime.
In the debates at the time of the adoption of the Constitution, an open issue which was not resolved was precisely the one that was addressed in #78, and in Marbury, and that is still being debated today. Where does the FINAL decision lay? Is it with Congress? Or with the Court? Or does it lie in the Executive?
Nobody had an answer to that.
If you read #78 carefully, you will see that Publius writes that the Supreme Court would strike down unconstitutional laws, but there's an implicit assumption that Congress wouldn't really pass them. That is why the discussion is confused, and why there is confusion between 78 and 81. Similarly, Madison initially debated AGAINST having a Bill of Rights, because he said that enumerating rights would IMPLY that there were others that the government could take. But by the time of adoption, seeing the ferocious resistance to the new Constitution across the republic because so many people simply did not TRUST the Constitutional project without a Bill of Rights, which is to say they did not AGREE with Madison and with those who said that everything would be fine without one, Madison came around to the position that a Bill of Rights was necessary.
We should remember that when The Federalist was written, it was written by partisans of the new Constitution. It was by no means a sure thing that it was going to be adopted. It might be rejected. They wrote to CONVINCE people that it was a good thing. They did not write with the sort of lofty authority of hindsight or the detachment of an historian. They were advocates of a position. In short: the Federalist Papers are PROPAGANDA for a cause. That's not to say that they are to be rejected. It is to say that where the new Constitution had holes in it...like "What happens if there's an unconstitutional law passed by Congress", the Founders had no good answer for that. They didn't really KNOW. So, the Anti-Federalists wrote, essentially, that the new government was sure to grow very powerful and start doing unconstitutional and intrusive things...and they proved to be right. And the Federalists wrote that the new Constitution would address those abuses through various means, like the courts and elections, and they were also right.
So, the real answer is that the Federalist is confused on judicial review, and on political parties, and on the authority of the President, and on a lot of other things, because they weren't fortune tellers but advocates of a position, trying to argue that everything would work out alright. Pressed into the corner, the Federalist paper authors said that judicial review would prevent Congress from abusing power. And they also wrote that Congress could limit the court from abusing power. And the two things simply stand in conflict.
They didn't know.
American experience with the law was similarly in conflict.
In the English Common Law, there is no judicial review of Parliamentary acts to strike them down for unconstitutionality, and the Parliament can amend the British constitution by a simple majority vote, like any other law.
But the American colonies' legislatures' acts WERE subject to being struck down by a superior court, the British Privy Council, which sometimes nullfied acts of the colonial legislature on the basis that such acts were incompatible with traditional English rights and liberties.
For example, when Pennsylvania's Quaker-dominated legislature passed an act in the early 1700s that prohibited slavery in Pennsylvania, it was struck down by the Privy Council on the basis that it violated the liberties of Englishmen by abridging their property rights. Had the English Parliament passed the identical act in England, then or today, there is NO appeal to any judicial power. Then, the King could have vetoed it, but that was the only check on Parliament.
So, which model were the Americans following?
To be frank, neither. They didn't like the Privy Council, but they were also afraid of Congress abusing its power (hence the Bill of Rights).
So, my view on the conflict in the Federalist papers, in a nutshell, is that the view of the Founders on exactly how the Judiciary would be a check on Congressional abuse was muddy. They didn't know how it would work out, and mainly assumed that Congress was limited enough to not be able to abuse power. Most Americans didn't buy the Founders' arguments on that, and didn't have enough faith to adopt the Constitution on the Founders' terms, but demanded a Bill of Rights.
And when partisanship roared to fore, contrary to all sunny predictions in the Federalist papers that party spirit would be muted, it was found after the 1800 election that some arbiter was wanting between an Executive controlled by one party and a Congress partly controlled by a bitterly opposed party. The Supreme Court became the referee, in Marbury v. Madison, many people were angry, but the ad hoc solution sufficed, and so they went with it. Some had thought it would work that way. Others had not. And still others opposed the very thought of it.
In 1788, when The Federalist was being written, it was only dimly seen that the Supreme Court might serve such function. It may never have. If, for example, the Federalists had won the election of 1800, things might have gone in a very different direction, and a long tradition might have been established of the US Supreme Court being like the high court of England, and not a political branch.
Was the Supreme Court INTENDED as a check on Congress in 1787?
The only answer that one can come up with is: by some, not by others, and most didn't think the issue was a real one, because they were focused on other pressing things.