So my former supervisor did the archaeobotanical work for Troy. Or part of it at least. I asked her and this is what she said:

Well, there are hundreds of books dealing with the "excavation of Troy", and it rather depends on your needs what would be recommendable. If you are looking for scientific details under the Korfmann excavations, I would suggest you have a look at the Studia Troica journal series, as well as at the Studia Troica monograph series.

And if you wanted more specific details, like for vegetation, faunal remains or something, I could see about that too. However, since there is such a large body of published work I suggest you start with the Studia Troica monograph series. At the very least work like that will direct you to other bits of work. Hope that helps. If you have a specific topic in mind let me know and I'll see what I can do.