Hi
You have a problem with USB - you need to show the USB interface on your HW and also the clock used.
If it isn't possible to generate an accurate 48.0000MHz USB clock this is the behavior expected.
For example, I see in your clock_config.h this
#define BOARD_BOOTCLOCKRUN_CORE_CLOCK 95977472U /*!< Core clock frequency: 95977472Hz */
96.977472MHz is not suitable for USB operation and will fail - where does this define come from??
Are you trying to use FEE (which is not possible with USB) rather then PLL based on a suitable oscillator or crystal?
Regards
Mark
uTasker project developer with experience of > 100 Kinetis based industrial/consumer product developments in > 20 countries.