"You are going to have to show me the exact words that you believe show that Jefferson acknowledged that the the 1st and 10th Amendments were intended to delegate government power to address religious issues uniquely to the state governments."
Starting with the OP:
"3. Resolved that it is true as a general principle and is also expressly declared by one of the amendments to the constitution that ‘the powers not delegated to the US. by the constitution, nor prohibited by it to the states, are reserved to the states respectively or to the people’: and that no power over the freedom of religion, freedom of speech, or freedom of the press being delegated to the US. by the constitution, nor prohibited by it to the states, all lawful powers respecting the same did of right remain, & were reserved, to the states or the people..." --Thomas Jefferson, Kentucky Resolutions, 1798. http://tinyurl.com/oozoo
1st Amendment: Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
10th Amendment: The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.
The Kentucky Resolutions extract above is a general example of the 1st and 10th Amendment division of certain powers between federal and state governments. A religion specific example from Jefferson's letter to Rev. Samuel Miller is as follows:
"I consider the government of the United States as interdicted by the Constitution from intermeddling with religious institutions, their doctrines, discipline, or exercises. This results not only from the provision that no law shall be made respecting the establishment or free exercise of religion, but from that also which reserves to the states the powers not delegated to the United States. Certainly, no power to prescribe any religious exercise or to assume authority in religious discipline has been delegated to the General Government. It must then rest with the states, as far as it can be in any human authority." --Thomas Jefferson to Samuel Miller, 1808. http://tinyurl.com/nkdu7
(Note that Jefferson's terms "United States" and "General Government" are references to the federal government, not the state governments. Part of the problem concerning c&s separation controvercies is that "United States" is now synonymous with both the federal and state governments. Failing to distinguish between federal and state governments undoubtedly helps to water down the meaning of the 10th A.)
The Miller extract shows that Jefferson broke tradition with Presidents Washington and Adams by "passing the buck" for the official government recognition of a national religious holiday, Fasting and Prayer I believe, from the federal government to the state governments. The constitutional provisions that Jefferson refers to are reasonably understood to be the 1st and 10th Amendments. Jefferson's Miller letter is also an example of Jefferson upholding a promise from his 2nd inaugural address concerning his determination to respect the constitutional division of federal and state powers, particular the unique power of the state governments to address religion:
"In matters of religion, I have considered that its free exercise is placed by the Constitution independent of the powers of the general government. I have therefore undertaken on no occasion to prescribe the religious exercises suited to it; but have left them as the Constitution found them, under the direction and discipline of State or Church authorities acknowledged by the several religious societies." --Thomas Jefferson: 2nd Inaugural Address, 1805. ME 3:378 http://tinyurl.com/jmpm3
Finally, Jefferson reflected on the 10th Amendment powers of the states by noting that the state governments alone had been trusted with the care of our religious freedoms as evidenced by this extract:
"Our citizens have wisely formed themselves into one nation as to others and several States as among themselves. To the united nation belong our external and mutual relations; to each State, severally, the care of our persons, our property, our reputation and religious freedom." --Thomas Jefferson: To Rhode Island Assembly, 1801. ME 10:262 http://tinyurl.com/onx4j
The problem with respect to properly understanding our constitutional religious freedoms is that, in contrast to the 1st Amendment's clear prohibition of religious powers on the federal government, people typically question why the Constitution seemingly says nothing about the power of the states to address religion. (Note that the 10th Amendment doesn't mention any particular power.) People consequently fall into the trap of presuming, with a little bit of help from Justice Black's treasonous interpretation of the establishment clause, that the Constitution "reasonably" meant for the states to be prohibited from addressing religious issues as well.
But what most people, including me, have overlooked is that the Constitution's silence about religious powers being prohibited to the state governments is what actually triggers the 10th Amendment to automatically reserve this power to the state governments. These powers are said to be reserved to the states because the states had this power before they established the federal government and its Constitution.
It seems like people are bickering about the establishment clause so much that they've essentially forgotten that the 10th Amendement exists.