Hi,
I see no USB OTG connections on USB_DP2/DM2 (which is the main CubeProgrammer interface) nor crystal on HSE pins (mandatory for USB).
Notice that for STM32MP MPU products, JTAG/SWD is only used for debugging and not used for Flashing. So cubeProgrammer does not connect using STLINK but rather using USB DFU on USB_DP2/USB_DM2 pins (I remind that HSE clocking is mandatory for USB to work).
For good start point before doing a custom board, please have a look to AN5031 and also to development boards EV1 or DK2 schematics.
I also recommend to read MPU wiki and FAQ (here and here)
Regards.
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