No article yet exists on this topic. Below are references from Thomas Jefferson's writings on Jews and Judaism, compiled by Monticello researchers.
Primary Source References
1787 August 10. (Jefferson to Peter Carr). "But those facts in the bible which contradict the laws of nature, must be examined with more care, and under a variety of faces...For example, in the book of Joshua we are told the sun stood still several hours...The pretension is entitled to our enquiry, because millions believe it. On the other hand you are Astronomer enough to know how contrary it is to the law of nature that a body revolving on it's axis, as th earth does, should have stopped, should not by that sudden stoppage have prostrated animals, trees, buildings, and should after a certain time have resumed it's revolution, and that without a second general prostration."
1818 May 28. (Jefferson to Mordecai-Manuel Noah). "your sect by it's sufferings has furnished a remarkable proof of the universal spirit of religious intolerance, inherent in every sect, disclaimed by all while feeble, and practised by all when in power. Our laws have applied the only antidote to this vice, protecting our religious, as they do our civil rights by putting all on an equal footing, but more remains to be done...Nothing I think would be so likely to effect this as to your sect particularly as the more careful attention to education, which you recommend, and which placing it's members on the equal and commanding benches of science, will exhibit them as equal objects of respect and favor."
1820 August 4. (Jefferson to William Short). "That sect had presented for the object of their worship, a Being of terrific character, cruel, vindictive, capricious, and unjust...Moses had either not believed in a future state of existence, or had not thought it essential to be explicitly taught to his people."
1820 September 1. (Jefferson to Jacob De La Motta). "[Discourse of De La Motta] excites in him [Jefferson] the gratifying reflection that his country has been the first to prove to the world two truths, the most salutary to human society, that man can govern himself, and that religious freedom is the most effectual anodyne against religious dissension...He is happy in the restoration, of the Jews particularly, to their social rights, and hopes they will be seen taking their seats on the benches of science, as preparatory to their doing the same at the board of government."
1826 January 6. (Jefferson to Isaac Harby). "Nothing is wiser than that all our institutions should keep pace with the advance of time and be improved with the improvements of the human mind. I have thought it a cruel addition to the wrongs which that injured sect have suffered that their youths should be excluded from the instructions in science afforded to all others in our public seminaries by imposing on them a course of theological reading which their consciences do not permit them to pursue, and in the University lately established here we have set the example of ceasing to violate the rights of conscience by any injunctions on the different sects respecting their religion."