In chapter 9 Wheelock mentions that hic and ille can both mean ‘he’ but can iste also be used this way? Is there a difference in meaning or emphasis as compared to using ‘is’ to mean he?
Yes, it can. It’s usually, IIRC, emphatic and often contemptuous. If the prosecutor said, gesturing at the defendant, “She did it!” that might be a time for iste.
As far as the others are concerned, if you recall the “core” meanings of the pronouns (he, this [one], that [one]" but also remember that a literal translation will often be too much, you won’t find it hard in practice.