1. As we should. The five letters to and from Schuller are 58, 63, 64, 70, 72. In Letter 58, Spinoza addresses his letter to Schuller, but its philosophical substance is a response to a letter Tschirnhaus had sent him via Schuller, in Letter 57. He relies on Schuller to relay his response. Similarly in Letter 63, Schuller is the nominal author, but the philosophical substance of the letter comes from Tschirnhaus. All the letters to or from Schuller are like that. In the correspondence which has come down to us, Schuller is no more than a representative of Tschirnhaus. This seems also to have been the view of the OP editors, who grouped the letters to and from Schuller with the Spinoza-Tschirnhaus correspondence.
2. On 8 April 1670 the Utrecht Church Council of the Dutch Reformed Church had condemned the TTP as a “profane and blasphemous book,” against which the burger-masters are urged to take “appropriate measures.” See Freudenthal/Walther 2006, I, 287. Violent reactions in other towns quickly followed. See Continuum Companion 2011, 25.
3. This correspondence was conducted through Jacob Ostens, to whom Letters 42 and 43 are nominally addressed. The situation is similar to that between Spinoza and Tschirnhaus.
4. Van de Ven notes that Van Velthuysen publicly acknowledged this in the preface to his Opera omnia (1680), where he wrote that while Spinoza was alive, he had many conversations with him (Van de Ven Facts, ch. 9).
5. Rom. 9:19–24, cited in Letter 75 (IV/312). There is useful commentary in the Anchor Romans. In other letters Spinoza uses other examples. For example, in Letter 73 (IV/307) he cites Paul’s speech to the Athenians (Acts 17:22–31)—with its statement that “in God we live and move and have our being”—which he takes as expressing an idea similar to his own doctrine that God is the immanent cause of all things. Fitzmyer (Anchor Acts, 610) comments that this line, apparently derived from Epimenides, “is not a pantheistic formula” in Paul, and that “it merely expresses the dependence of all human life on God and its proximity to him.” Arguably, the same is true of Spinoza’s use of this formula.
In Letter 58 (IV/268) Spinoza refers Tschirnhaus to II, vii, of CM (where he had cited Romans and Isaiah) and to Descartes’ Principles I, 39–41 (where Descartes had confessed his inability to reconcile God’s omnipotence with an indeterminist conception of freedom).
6. Rom. 1:20, 2:1.
7. This issue arose also in the correspondence with Tschirnhaus (Letter 57, IV/264), where it got a similar answer, crisply expressed: “evil men are no less to be feared, nor are they any less harmful, when they are necessarily evil” (Letter 58, IV/268).
8. This was church doctrine as early as the Council of Chalcedon in 451. Cf. Denzinger 1954, 60–61.
9. For a good brief discussion of Tschirnhaus’s life and works, see Schönfeld 1998. For a more detailed account of his work on method, see Van Peursen 1993. Tschirnhaus’s Medicina mentis is now available online. See Tschirnhaus 1695.
10. Leibniz to Oldenburg, in Leibniz, Gerhardt, 143, as quoted in Laerke 2008, 363.
11. I discussed this in Curley 1969, ch. 4.
12. On this, see Curley 1990a and especially Laerke 2008.
13. In Curley 1990a I tried to make an educated guess about this.
14. See Letter 72. Spinoza’s attempt to deny Leibniz access to the manuscript of the Ethics was apparently fruitless, since it seems that Tschirnhaus did share a copy with him. In the end Spinoza agreed to meet with Leibniz when he visited The Hague late in 1676, only a few months before Spinoza’s death. By that time Leibniz had procured a copy of the Ethics and they discussed it. See Laerke 2008.
15. See Steenbakkers 1994, 62–63.
16. Gebhardt/Walther 1998, 248–49, italics in the original.
17. In the letter the condition is that Spinoza would have “the utmost liberty to philosophize,” with the understanding that he would “not abuse this freedom to disturb the publicly established religion.”
18. Wolf 1966, 441–42.
19. Gebhardt/Walther 1998, 252.
20. See Nadler 1999, 311–14.
21. Boxel was the secretary of Gorinchem from 1655 to 1659, and pensionary of that town from then until he was dismissed from that post in 1672. The Continuum Companion conjectures that his dates were 1607/12? to 1680? (2011, 27).
22. It is now easier to understand Van Velthuysen’s position from the recent edition of his defense of Hobbes (Van Velthuysen 2013). See particularly Secretan’s introduction to that text.
23. On this, see Price 1994.
24. See TTP xix, and the annotation there regarding the Remonstrant controversy.
25. Spinoza protests against this common interpretation in Letter 43, IV/223b/22–25.
26. For further information, see Nadler 1999, 336–40, and Meinsma 1983, passim, but especially 451–58.
27. For more on Steno, see Kardel 1994 and 2013. Cutler 2003 provides a good popular account of Steno’s scientific work.
28. Cutler 2013, 161. Mogens Laerke tells me (in personal correspondence) that this probably does not fairly represent Leibniz’s view of Steno.
29. On these matters, see Curley 1990a.
30. Van de Ven reports that Van Velthuysen’s critique was “actively disseminated” among Spinoza’s critics and admirers. See Van de Ven Facts, ch. 9.
31. See Freudenthal 1899, 231–32; Gebhardt/Walther 1998, 140.