Do you have any kind of flywheel on your motor shaft? That can help achieve faster stepping speeds. What do you have VREF on your driver set to?
The DRV8825 motor driver has a higher absolute maximum voltage than the A4988 (45V instead of 35V), so you might be able to use one with a 36V power supply to get faster speeds. Also, our 42mm Sanyo pancake stepper motors seem to have a little higher stepping speed than the 50mm one you are using right now, though it is not clear to me you would be able to get the speed you need out of them. You might look at the pull-out torque curves in the datasheet for them to try to judge for yourself whether they might work (on that datasheet, 5,000kpulse/s is 1500rpm).