First we will start with material from TC-Alternate posts, two are copied over, two are urls.
[TC-Alternate-list] history of the Newton "notable corruptions" letters[TC-Alternate-list] Newton's 3 letters - heavenly witnesses, God was manifest, short miscellany
Steven Avery - Sept 21, 2011
The first two letters cover the two verses, 1 John 5:7 and 1 Timothy 3:16, they are often published as one unit. The Horsley edition is considered correct, not the earlier one that says it is to Mr. Le Clerc. The two letters are published in a number of places, HTML and google books, including the editions from the Jared Sparks essay collection. Here are three editions in addition to the one you have below.
Isaaci Newtoni Opera quae exstant omnia, Volume 5 (1785)
The recorder: tracts and disquisitions, (1803)
A collection of essays and tracts in theology, from various authors,with biographical and critical notices , Volume 2 (1823)
The third letter was in these books, SNIPPET, beginning on p.129.
The Correspondence of Isaac Newton , Volume 3 (1977)
Newton had additional textual verse errors in the third letter:
Here you go, you can catch more Newton errors falling to the ground like an apple here:
The Third Letter
Newton's Religious Writings
Various drafts and copies of the Two Notable Corruptions of Scripture and related material.
[TC-Alternate-list] Newton Letters - Simon's influence, historical follow-up[TC-Alternate-list] Re: history of the Newton "notable corruptions" letters
Some Richard Simon material was in English in 1689. And fully in French.
So the dates seem more than simply coincidental.
Critical History of the Versions of the New Testament (1689)
http://books.google.com/books?id=bds7AAAAcAAJ&pg=RA3-PA105 (sample on verse p. 105-107)
So Newton could use that and stumble through the in depth critical writing in French:
Histoire critique du texte du Nouveau Testament: (1689)
Newton references Simon on the Stephanus manuscripts (in the Horsley edition). I think it is a stretch to see those sections as written by anybody other than Newton, although possibly not in the first draft (noting your timeline below) .. or the version sent to Locke.
As with the Vulgate Prologue and the Athanasius dialog with Arius and other documents, the higher burden of evidence should be on the idea that the first-person writings were put in with deceptive intent by third-parties unknown. Such ideas need more than evidence circumstantial, for many compelling reasons (Glenn Miller discusses this idea in terms of ancient documents including the Gospels quite nicely, Roger Pearse as well for the early church writers.)
Thus, I have to go, for now, with the idea that the Richard Simon references are at least from Newton. Maybe in 1690, maybe a spot later.
Two Notable Corruptions (Horsley edition)
For Father Simon tells us, "That, after a diligent search in the library of the king of France, and in that also of Monsieur Colbert, he could not find it in any one manuscript; though he consulted seven manuscripts in the king's library, and one in Colbert's."
See p. 192, 196 and p. 204 for more references.
We could check and see if that info was in the English edition.
So what is the basis for thinking that Newton had not consulted Simon ?
This article by Ron Iliffe discusses some of their similarities and differences.
Scripture and scholarship in early modern England (2006)
Friendly Criticism: Richard Simon, John Locke, Isaac Newton and the Johannine Comma
What you have below is interesting, and complex. Thanks for putting it together. It would be interesting to pursue this further, and I accept that, for now, you have raised good issues about exactly what was in the original letter.
On the other hand, I do not see much of great sophistication in the Newton letter, and, before publication, he may have simply been concerned by how badly Simon's contra ideas were being torn apart in the marketplace of textual ideas (not mentioned by modern writers).. and decided not to get in the middle of a very difficult fray. Along with the doctrinal baggage issues, which could definitely affect his position.