Denniston's "The Greek Particles" is a good reference; focused on classical stuff. More of a catalogue than a discussion/examination, though. That said, I have benefitted from it, particularly in its treatment of αλλα.
Runge's "Discourse Grammar of the Greek New Testament" has a good discussion on conjunctions in chapter two.
Heckert, "Discourse Function of Conjoiners in the Pastoral Epistles" is a good treatment of the function of the most common conjunctions in the Pastorals; the work applies well outside of the Pastorals as well.
Levinsohn, Stephen H., "Discourse Features of NT Greek" provides more information on the framework that both Runge and Heckert use, but it can be tough slogging. Also note Levinsohn's "Textual Connections in Acts".
Hope it helps. At the get-go, I'd say Runge and Heckert provide the most practical information; Denniston is useful but more like a reference grammar is useful.
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