Hello Caden,
FTM0 is used by the Timer module (..\PLM\Source\TMR\) on channel 0.
The task scheduler (TS) kernel is not using the FTM0 module but it receives events from the timer module (which uses FTM).
If you reconfigure the FTM0 module then the Timer module will be affected and the thus the entire system.
Another observation is that PORTD is not clocked by the FTM but the peripheral clock (which comes from the MCG module).
My recommendation is to use a different FTM module (FTM1 or FTM2).
Or you may try to reconfigure the Timer module to use the FTM1 instead of FTM0 (..\PLM\Interface\TMR_Interface.h)
Hope this helps.
Regards,
Mihai.