Hi Aaron,
For checking and changing Cortex-A9 CPU frequency in u-boot, refer to the below files:
u-boot/arch/arm/cpu/armv7/am33xx/clock_am43xx.c
u-boot/arch/arm/cpu/armv7/omap-common/clocks-common.c
u-boot/board/ti/am43xx/board.c
You can check registers PRCM_CM_CLKSEL_DPLL_MPU (0x44DF2800 + 0x560) and PRCM_CM_DIV_M2_DPLL_MPU (0x44DF2800 + 0x570) from the u-boot prompt with "md" command and thus get M,N and M2 values. Then you can calculate the CPU frequency according to the formula provided in AM437x TRM (section 6.6.3 ADPLLS).
You need also define what is the DPLL_MPU input frequency. It is based on main OSC frequency, which is 24MHz on the TI EVM.
Regards,
Pavel