Answer from cs61c-au (Robert Webb 14343043) for Question 1
If there is no delay between the flip-flops, and the CLK of both are either simultaneously on or of, then one would expect that both of them would have the same value at any given time.  But there is delay inside the flip-flop, so the state of the second flip-flop would not necessarally change because the state only changes to the value of the input when the CLK is charged.