Controlling a Stepper-Motor with 2 H-bridges
Keep in mind that when you use NPN transistors on the "high side" of the H-bridge, you need to drive their bases to +12V, since they're functioning as emitter-followers. The emitters can't go any higher than one diode drop below the base voltage.

The better approach is to use PNP transistors on the high side, so that they can be put into saturation for minimal voltage drop and power dissipation. You can use NPN transistors driven by the 3.3V outputs of your controller to switch the PNPs on and off.