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Rupa
is "shape", "form", "object", "appearance", "image", usually in the sense of something perceived visually.
Kaya
is "body", both specifically of living being, but also generally a body of a tree (i.e. trunk), a body of a guitar (i.e. sound box), and even a body of a teaching (dharma-kaya).
Although in Theravada there is a tradition of using the word rupa to refer to "material" aspect of a living being, I would say "rupa" is more frequently used in the phenomenological sense ("what is perceived"), while "kaya" has more ontological flavor ("what is").