CKSO is not available on the MPC8240, MPC8241, or MPC8245 processors.
SRST can be deselected in favor of the SDMA12 signal used for Extended Addressing (except on the MPC8240 processor).
QACK is an output signal only, so it need not be connected to the COP header.
The USB TAP probe fully supports the MPC8240, MPC8241, and MPC8245 processors despite the absence of the signals mentioned above.