The schematic you posted shows an IGBT, not a BJT.
The problem with a BJT is that the current gain is probably less than 100 at a collector current of 3.3 A. That means that you need 33 mA or more to drive the base. The USB-6009 is limited to about 5 mA. You might be able to make it work with a darlington connected pair of transistors where the current gain would probably exceed 1000.
An IGBT or power MOSFET can be driven by a voltage source. The transition speed is limited by the current available to charge the gate capacitance but that will still be orders of magnitude faster than the software timed output.
A digital output in Active Drive mode can drive 8.5 mA. This is probably a better choice for PWM. You will still need more gain than a single transitor can produce and you will still be limited by the speed of the software timed output.
Lynn
