U.S. Constitution Article I, Section 8, clause 18 - The Congress shall have Power ... To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution in the Government of the United States, or in any Department or Officer thereof.
Sure, Congress has the power to make laws, but the Constitutional power to make laws does not give those laws equal or greater status than provisions of the Constitution itself. Laws inconsistent with the prerogatives expressly stated in the Constitution itself are invalid. That's the entire principle of judicial review.
I'm not claiming that the Judiciary Act of 1869 is unconstitutional. I'm saying that the interpretation you are attaching to it -- that the Senate
must confirm presidential nominees so as to keep the number at 9 -- is wrong. The power of advice and consent inherently includes the power not to consent, which mean that the number of sitting justices would be less than the number authorized by Congress. The Constitution both contemplates and permits this. So, the only Constitutionally correct interpretation is that there are nine seats to be filled, subject to the Senate's confirmation of people to fill those seats.
Every branch of government is bound to follow and abide by every lawful act of Congress enacted under their constitutionally-granted powers.
Well, let's cut to the chase: if Congress passed a law requiring the Senate to confirm a Supreme Court nominee within, say, six months, is that law binding and Constitutionally sound?