Hi Ryan,
Let me start off with saying that I'm certainly no expert when it comes to stepper motor control :-)
I have not implemented anything complicated or precision based personally.
For the conversation, I'll assume your stepper motors are controlled via PWM (Pulse Width Modulation).
(There are other type of motor control out there)
Unfortunately the Raspberry Pi only includes a single PWM pin.
This means that for a high precision solution, you will need some external peripheral device to provide additional PWM support.
This board includes the PCA9685 chip which provides 16 channels of PWM.
One of the community members (Christian Wehrli) contributed an Pi4J extension to support the PCA9685 chipset.
And here a a couple of code examples using this extension:
I hope this helps get you started :-)
Thanks, Robert