The hybrid module is probably not at fault here. The hybrid sends a signal to the power manager chip which indicates battery level. And the power manager chip sends a signal to the hybrid to tell it whether -5 volts should be generated or not. If that battery level signal droops too low your system will pop up a message saying something to the effect of "your battery is the weakest link, goodbye" and then the OS shuts down.
If main 5v rail regulation had failed on the hybrid, it's not likely that your system would be working at all.
CPU clock frequency comes from U10D, the "CPU Glue" logic chip. If the clock frequency is wrong, something might be up with the CPU Glue chip, the CPU Glue oscillator, or the "5/0" power rail (which powers both the CPU and clock oscillator). Check voltage on Q11's pin 2 (the big tab) near the CPU.