Hi Brad,
how did you change the Clock oscillator to Crystal?
Did you change the register configuration in pll_init() function?
K10 Datasheet describes register 25.7.1 OSC Control Register (OSC_CR)
SC2P: Add 2 pF capacitor to the oscillator load.
Header MK10X256VMD100.h has #define OSC_CR_SC16P_MASK etc.
Obviously there isn't any function for setting those.
I think you can set those in pll_init, e.g. set 12 pF caps:
OSC_CR = OSC_CR_SC8P_MASK | OSC_CR_SC4P_MASK
I use the bsp_twrk60n512_pe, it has the cap configuration directly in Component Inspector.
~Mark