Hello ives,
For your question , i have some suggestions :
1) Which version of KSDK do you use ? i recommend you use the latest one ksdk1.3, you can download it in the web.
2) If you want use the KSDK APIs configure the clock mode ,i recommend you sue the function "CLOCK_SYS_SetConfiguration()",
it configure the SIM SIM .etc clock module ,it include the function "CLOCK_HAL_SetFbiMode" ,you can find this function here :
Freescale\KSDK_1.3.0\platform\system\src\clock\MKL25Z4\fsl_clock_MKL25Z4.c
(in general , do not directly use the "HAL " functions, these HAL functions are call by the driver fucntions. )
3)If you do not want use the ksdk driver, in the file of "system_MKL25z4.c" and "system_MKL25Z4.h" have defined all of the clock mode ,
you can refer to :

4) You can also use the PE configure the clock , i thin it is easy .
If use the latest version still can not work well, please contact me without any hesitate .
Hope it helps
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Have a great day,
Alice