I tested the commands that @Barf posted above, and they all work great! In fact, the miniDSP 2x4 HD seems to respond faster when using the TSU9400 as compared to using the remote that came with the miniDSP.

For anyone looking to use a miniDSP, FYI, the miniDSP remote doesn't have discrete commands for the input sources (Analog, Toslink, and USB). The miniDSP remote only has the "Next Input Source" command. Using the miniDSP plug-in, it is possible to teach the miniDSP remote codes. So, I used some old codes from an NEC projector to teach the miniDSP commands for: Analog, Toslink, and USB. Strangely, once I taught the miniDSP these commands, it stopped responding to the "Next Input Source" command. But no big deal - I'd rather have the discrete input commands instead of the "Next Input Source" command.

@Barf, @Lyndel McGee, thanks for your help!!