The last sentence...
I said in class that there are three ways I can see taking key parts of the sentence (more as one adjusts certain words), but I'll restrict myself to the more probable two.
First is as Godfrey does: intuitus (not in Cassell's: it is a fourth-declension noun, rarely used, meaning a look or a view; L&S say that in the sense regard or consideration it is used only in ablative, but this work is out of the date range) is the subject. If that is the case, then I don't see that ille can modify anything else, or stand as a substantive. We have to note that there is one finite verb from Quae to cernit, and the et before suis starts a new clause. There is no conjunction nor any punctuation in the first clause. Therefore:
1. All which things (quae ... cuncta taken together, although quae is the relative pronoun and cuncta is the antecedent -- this is common -- and cuncta is simply everything; that is the intuitus sees everything), however, looking forth upon from eternity, that (ille) consideration (i.e., providence is doing the considering) of providence discerns, and disposes whatever is predestined by one's merits.
1.a. (preferable in many ways) That consideration of providence, however, looking forth from eternity, discerns all these things....
2. Which things (what has gone before), however, that consideration of providence discerns, looking upon everything (cuncta is now a neut. pl. substantive and not directly connected to quae) from eternity, and ....
But, ille is quite removed from intuitus, and so intuitus could be acc. pl., and the object of cernit, whose subject is ille, God:
3. But God, however, looking upon all these things (all which things--quae being what has gone on before) from eternity, discerns the view of providence and ....
