[catacon]

Calibrating the speed controllers is a good start. You can use an encoder to get the speed of each and tune a PID controller to run them both at the same speed. If you are using Talon SRXs, you can run one Talon as a follower so it will take the same input as another. This may be useful if you can only encode one lead screw. However, if the drives are (significantly) mechanically different, this will not solve you problem.

The "easiest" way around this, is to mechanically couple them. We have two ball screws this year: one on each side of the robot. We have a drive shaft running across the robot that couples them together. We are only encoding one ball screw and running two Talon SRXs in a leader-follower system.