Why do we wave the chicken over our heads during Kaporat? In the Mikdash we would Lean on animals, so why do we wave them over our heads?

I don’t know for sure the reason for the waving; maybe to illustrate the fact we are replacing the chicken with ourselves. The leaning, on the other hand, is only done with offerings in the temple, the Kapparot are not a sacrifice, they are a symbolic custom the shows us what we may deserve for our bad deeds and a mitzvah of Tzedakah to the poor.