Note that we need the width of PRESET pulse, CLEAR pulse etc to be greater than some minimum values for proper operation of every flip-flop. This width is measured between 50% transition points of rising and trailing edges of the given signal.
Setup and Hold time are measured w.r.t the activating clock edge. The Setup time is the difference between the 50% transition point of DATA input before clock edge and 50% transition point of activating clock edge while Hold time is measured between 50% transition point of activating clock edge and 50% transition point of the DATA after clock edge as shown below:
Propagation time is measured between 50% transition point of activating clock edge and the 50% transition point of output for the corresponding edge but it is generally different when output changes from 1 to 0 or 0 to 1. Hence we define propagation time TpHL as difference between 50% transition point of activating clock edge and 50% transition point of the output change from HIGH to LOW
while propagation time TpLH as difference between 50% transition point of activating clock edge and 50% transition point of the output change from LOW to HIGH.
And we take average of both TpHL and TpLH to specify the propagation time