Isaac Newton's theological writings remained in his family's possession until 13-14 July 1936, when they were sold in an auction at Sotheby's (London). The most significant portion of the theological papers is now part of the Yahuda Collection, Jewish National and University Library, Jerusalem.
A.S. Yahuda (1877-1951) had taught in Germany and Spain before World War II, and then fled to England, and finally to the United States in 1940. He was not present at the auction in 1936, but managed to assemble his collection by purchasing manuscripts from others who had attended.
Yahuda was a strong anti-Zionist, but he left his collection to the library in Jerusalem, in part because it also included a good deal of material related to the Middle East. Yahuda's family opposed the bequest, but in 1969 Newton's theological papers were finally shipped to Israel.
Newton's ‘rules for interpreting the words and language in Scripture’
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You can see many of these manuscripts on line, at a number of different sites, especially at http://www.newtonproject.sussex.ac.uk, and more specifically at http://www.newtonproject.sussex.ac.uk/prism.php?id=94&loc=6&sr=1. There is also http://www.isaacnewton.ca/, a Canadian site; and even in Hebrew, http://jnul.huji.ac.il/dl/mss/newton/exhibition.html.