Hi @Vamshi_,
1.
Do not modify the modeConfig structure at runtime.
The configuration must be done in the .mex file, and Power_Ip_aModeConfigPB[1] should be used when calling Power_Ip_SetMode().

To verify the selected power mode, enable CLKOUT and measure the BUS_CLK frequency on that pin.
2.
Just configure and enable the GPIO interrupt, that is all.
In STOP mode, the NVIC is not active. It is replaced by the AVIC.
3 & 4.
If V_GPIO > VDD + Vf, the MCU can be unintentionally powered through the GPIOs, since all GPIOs are clamped to VDD.
To prevent this, R59 must be removed. However, you must then ensure that the MCU is properly powered through connector J19.
Additionally, keep in mind:
- GPIO outputs driving external loads will increase overall MCU VDD power consumption.
- No GPIO input should be left floating.
Regards,
Daniel