Well in designing my 5x5x5 led cube, I used a 2 millisecond timer interrupt to set-up my scanning of the cube, so five levels at 2 millisec each gives me a 10millisec update cycle time and I detected no flicking at all. As far a ma drive level for the leds Vs scan rate, I simple used shift registers that contain built in constant current (sinking) output pins which made the whole brightness thing a no worry situation. Each 16 bit register (I used 2 series connected) uses a single 'programming' resistor to set the desired constant output current value for all the output pins (I set for 20ma) and the performance is great, led brightness is the same no matter if a single led or all 125 are being lite up.
Lefty