I think it's safe to say that the AFE Y-pipe will be incompatible. That entire section of the stock exhaust will be replaced with the turbo kit. It has its own 2-into-1 pipie heading up toward the turbo in front of the engine. Then a single pipe heads down from the turbo and back to connect with the remainder of the stock exhaust.

I haven't seen how the pipes are routed in the 3.6 kit yet, but I think it will be along the same lines as the 3.8 kit pictured here: