Hey @SidMishra
Just to confirm that you're able to talk to the MCU for programming and debugging?
I presume you're referring to the SPI CLK which should be generated by U1 and going through U18 on its way to the K20 (U16)? Have you scoped it from U1 to U18 and then from U18 to U16?
If it's a problem from U18 to U16 then I would first check the voltage level on U16's S (Pin 1) to make sure the right output is selected. If it's not that, check your pin mux value for U18's Pin 77 (PTC5) - could it be a GPIO output instead of a SPI CLK (which makes it a high impedance input).
Good luck!