Regarding (5): The framers in fact rejected a previous iteration of the language of the 10th Amendment that would have reserved to the states any powers not expressly delegated in the Constitution. So we know that's not what they meant.
Yes, I agree that the states were not delegated all powers not expressly delegated by the constitution, but "the people and the states" were. I have never heard a better explanation for the 10th amendment than to say that it was restating the enumerated powers doctrine (though I cannot recall where I first heard that explanation). If you have a better explanation of the 10th amendment, I am very interested to learn what it is.
Regarding your second point: the change was not "states" vs. "people and the states". The change was whether the rights referred to were solely those expressed in the Constitution, or something broader. Broader won. This is an argument you are going to need to take up with the authors of the Constitution, because they do not agree with you.
2) I agree that Congress created the Customs Service to carry out an enumerated power according to laws passed by Congress, and would say that the Navy, Internal Revenue Service, and Treasury were created in a manner compliant with the constitution (and its amendments). Health and Human Services, Housing and Urban Development, and the Department of Education are not compliant with the Constitution.
3) I agree that searches of foreigners at the border are not even required to be reasonable, and searches of citizens must only be reasonable. Reading people's correspondence without a warrant was never considered 'reasonable', and I have no evidence that 'metadata' was considered less important than the contents of the correspondence. There is also no provision for 'collecting and storing information about citizens, but not looking at it unless you really want to'.
4) According to my reading of the Constitution, Congress must establish the laws/rules for the collection of revenue, and fund/authorize the relevant agency. After Congress does this, it is the President's job to "take care that the laws be faithfully executed", which I interpret as meaning that they should hire and supervise people to do the job Congress told them to do.
5) I sympathize with your view, but the entire Bill of Rights was meant to be a dead-letter by that definition. I am sure you aware that some founders made the case that the Bill of Rights was entirely superfluous, as the federal government had never been given the power to regulate speech or firearms, search citizens arbitrarily and invasively, force them to confess to crimes, or forcibly station soldiers in their homes. Unfortunately, the Bill of Rights has proven to be vital (if insufficient) to the preservation of liberty.