Hi Mehdi,
The BSPCloning tool is perfect for this scenario.
Clone the superset BSP (in your case from the TWR-K60D100M), enable the PE component in the BSP using CW, add a CPU component for your specific Kinetis device, tweak and tune as needed.
Documents to look at:
~Freescale_MQX_4_0_2\doc\tools\MQX_BSP_Cloning_Wizard_Getting_Started.pdf
~Freescale_MQX_4_0_2\doc\tools\cw\Howto_SetupKinetisClock_UsingPE.pdf
So once the new CPU component is added and clocks setup accordingly, generate code, and now PE code over rides the default MQX clock init code.
Regards,
David