1. The Madison quote is true but not relevant. The SCOTUS does not have "all powers, legislative, executive, and judiciary".
2. The Jefferson quote is specifically talking about SCOTUS usurping power from the executive branch, not about their general power to determine the constitutionality of laws set before them for review by the judicial process. It would be instructive for you to read the entire letter from which that quote was taken--or at least the entire paragraph because it has a lot of good information.
http://rotunda.upress.virginia.edu/founders/default.xqy?keys=FOEA-print-04-01-02-0348 It clearly states that each branch has the power to determine constitutionality and act in its own sphere based on that determination with the powers afforded it, but that each branch has limited power over the other branches.
"...the judges, believing the law constitutional, had a right to pass a sentence of fine and imprisonment..." Clearly Jefferson says that they are afforded the right to determine constitutionality and act on that determination.
"...but the Executive, believing the law to be unconstitutional, was bound to remit the execution of it; because that power has been confided to him by the constitution..." Just as clearly, Jefferson indicates that the Executive is also bound to make determinations and to act on his determination of constitutionality.
"...the opinion which gives to the judges the right to decide what laws are constitutional, and what not, not only for themselves in their own sphere of action, but for the legislature & executive also in their spheres, would make the judiciary a despotic branch." But here's where the problem arises. When they operate in their own sphere of action they are ok, it's when they also start to try to control the other branches of the government that the problem arises.
Furthermore, it clearly addresses your contention that constitutional rights may not be regulated at all. Jefferson clearly spells out the intent of the framers to allow some reasonable restrictions on constitutional rights, albeit by the state legislatures more than by Congress.
"...we deny that Congress have a right to controul the freedom of the press, we have ever asserted the right of the states, and their exclusive right, to do so."
3. I'm not sure what you intended to convey by including the Hamilton quote. It clearly states that the courts can rule on the constitutionality of laws, a point which seems exactly counter to your arguments.
What is being proposed here by a couple of highly educated folks is that we fought a revolution for nothing?
Nobody is "proposing" anything. Stating how things are is not a proposal or endorsement, it's simply an observation of fact.
That in the end, we are not really a representative republic but instead a nation under rule of a monarchy of 9 lawyers in black robes sitting on the SCOTUS?
That's a stretch. SCOTUS can not create law, it can only rule on the legality/constitutionality of existing laws created by the legislature or of actions performed by others. Nor does it have the powers of the Executive branch.
It may or may not be true that it has more power than the framers intended, but it's a long way from being a monarchy and the U.S. is obviously still a representative republic.