Since you are using different GPIOs other than which are used in the firmware (53-56), did you take care to update the IO Matrix?
If you have already taken care of the following then you may need to observe what is happening on the SPI bus. (I have checked from the datasheet of the SPI Flash that the commands related to READ_STATUS, READ, PROGRAM are same as the ones used in the firmware).
Thank you for the reply.
GPIO muxing is done properly. I'll look into SPI bus.
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