The default setting of J109\J110\J111 connect 1-2, but should be 2-3 in order connect the signals to GRB LEDs.

Try to connect 2-3 of J10, power the VDD of MCU by P5V0.

Due to the D1(RESET_S32K) is glowing, you may need to halt the MCU by P&E Recovery Utility and then program it. You can refer: Can't use PEmicro debugger with S32K118EVB2-Q048
I didn't find other difference, so you can use:
S32 Design Studio for S32 Platform Version: 3.4
S32 Design Studio S32K1XX SDK RTM 4.0.2
Remember Switch package for the Processor and Update Codes.

Best Regards,
Robin
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