Exit from stop is done by asserting reset, any enabled asynchronous interrupt, or the real-time interrupt. The asynchronous interrupts are the KBI pins, LVD interrupt, ADC interrupt or the ACMP interrupt.
Notice that the real-time interrupt is what wakes you up from Stop mode, not the timer/pwm or modulo timer. You need to look at Section 5.7 Real Time Interrupt, to figure out what interrupt period you could get (Table 5-7) using the 32.768kHz watch crystal as external oscillator. You will be limited to 8 choices for the real time interrupt period, which will wake you from Stop mode.
I can't tell what the RTI adder from stop would be with 32.768 external crystal from the data sheet.
I can suggest that you take a close look at the 9S08QE8, if low power is your main concern. It will cost a bit more than the RS08KA8, but will have much better numbers for power consumption.
Thanks,
Rick