Hi,
The changes you described (high-side current sensing, different gate driver architecture, PWM polarity changes, and the associated motor-control software adaptations) represent a significant shift from the MCSPTR2AK396 reference design and require substantial modifications to the reference solution.
Due to the project-specific nature and complexity of this work, we are unable to provide a complete migration guide through the standard support channel.
For dedicated assistance with adapting the reference software to your custom hardware, please consider engaging NXP Professional Engineering Services:
NXP Engineering Services
Best regards,
Petr