Hey kph. Just another quick note about the clock. BrianPack is correct - you can decide whether or not to export the clock in SW... just make sure you call "niHSDIO Commit.vi" after calling "niHSDIO ExportSignal.vi" to actually commit the settings to HW and physically stop the clock.
Making a clock signal out of a data line is a fairly common tactic when people need the clock to start/stop or want to produce a clock at a different rate than their internal sample timebase. The ExportSignal method depends on SW timing, while a clock on a data line can have very precise timing. The Digital Waveform Editor can be useful in helping you create your pattern to add clock and control signals to your data sets.
Another possibility would be that if your device has some kind of chip enable, you can use the DataActive to tell the device to pay attention to the clock. Alternately, you could AND the clock and the data active event externally.
Hope some of this helps.
Chris