You really thought this through.

Avoid using the suction cups. These might get gummed up causing stress on the animal and the animal may injure itself. The cups may also loose suction which would result in another problem, they would be on the animal in microgravity and they would not do anything.

You should make the waste flow in a method so as to avoid clumping up and blocking any further flow.

If I am reading the sketch correctly the water dispenser port is near the floor of the habitat. This port may get gummed up by waste or food. Try putting the port in the walls instead.