Answer from cs61c-ax (Amanda Alfonso 15906918) for Question 1
Well, I'm not entirely sure what is meant by "behaving as expected," though I can assert that the two flip flops should act somewhat independently.  By this, I mean that the input of the second flip-flop is a signal, which just happens to be the output of the first flip-flop.  Consequentially, the second flip-flop should operate with it's own output in response to the input signal and the clock cycle.