Very interesting project!
Pretty much everything is used today, although many notes are synthetic rather than natural. In your list, quince and lotus are probably the least common today. One less used ingredient that has gathered some attention recently is spikenard (or jatamansi).
You are probably aware of a reconstruction of an Egyptian perfume that gathered attention some time ago, that of Kyphi, which I think was sold at the Egyptian museum in Cairo.
Finally, you can check here and there (or ask) the blog perfumeshrine by Elena Vosniaki. She's a very knowledgeable Greek perfume specialist who often makes references to classical Greece.