Congress specifically has the power to limit the areas over which the Supreme Court and federal courts may rule. That authority has never been used, to my knowledge, but it is there in the text of the Constitution.
And "The Federalist" is hardly the only source of illumination on the intents of the writers of the Constitution. There was this little group called "anti-Federalists" who had other ideas--said ideas which resulted in the addition of the Bill of Rights.
Congress does not have the power to limit the jurisdiction of the Supreme Court only the lower courts. The Supreme Court has 'All Judicial Power in Law and Equity'. Congress can change the number of justices though.