Hi Andrew Barnes
In References manual you can find:

As you can see here, there are 3 modules that you need to configure to setup core clock and timer clock with external clock; System oscillator, MCG_lite and CLKGEN (SIM).
You mentioned that you have installed SDK 2.0, Have you tried driver_examples provided in this package? there is an mcglite example located in {SDK_2.0 path installed}\boards\frdmkl03z\driver_examples\mcglite. This example first uses BOARD_BootClockRUN function to set Core clock: 48MHz and Bus clock: 24MHz. And after it configures 4 different clock modes; HIRC mode, LIRC2M mode, EXT mode and LIRC8M mode.
In this example they use the following configuration for the the MCG_lite in the clock EXT mode:
mcglite_config_t mcgliteConfigExt;
mcgliteConfigExt.outSrc = kMCGLITE_ClkSrcExt;
mcgliteConfigExt.irclkEnableMode = 0U;
mcgliteConfigExt.ircs = kMCGLITE_Lirc8M;
mcgliteConfigExt.fcrdiv = kMCGLITE_LircDivBy2;
mcgliteConfigExt.lircDiv2 = kMCGLITE_LircDivBy4;
mcgliteConfigExt.hircEnableInNotHircMode = false;
CLOCK_SetMcgliteConfig(&mcgliteConfigExt);
And it uses the BOARD_InitOsc0(); to configure the System oscillator module, in this example it uses a external crystal:
void BOARD_InitOsc0(void)
{
const osc_config_t oscConfig = {.freq = BOARD_XTAL0_CLK_HZ,
.capLoad = 0U,
.workMode = kOSC_ModeOscLowPower,
.oscerConfig = {
.enableMode = kOSC_ErClkEnable,
}};
CLOCK_InitOsc0(&oscConfig);
CLOCK_SetXtal0Freq(BOARD_XTAL0_CLK_HZ);
}
And CLKGEN (OUTDIV1 and OUTDIV4) doesn't change. So, in this example they use the following path in this mode:

Your clock configuration depends in your application, but if you want to use external clock for core clock and timer you can take as base this example and use OSCERCLK for a TPM or a LPTMR. One thing to consider is that FRDM-KL03Z uses an external crystal, but if you just want to use an external oscillator in the EXTAL0 pin, you should change .workMode = kOSC_ModeExt. Also if you want to change the OUTDIV1 and OUTDIV4 you can set a new simConfig and use CLOCK_SetSimConfig(&simConfig);
I recommend you to check the Reference Manual (attached), chapter 24 and chapter 25.
Hope this information could helps you and if you have any other question please don't hesitate to ask us.
Have a great day,
Jorge Alcala
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