camow7,
This doesn't sound like something you would want to do with a daq 6009. If I'm understanding you correctly, you have a shift register that you would like to drive with two digital lines from your daq 6009 while also passing data from a third DIO line on the same device. If this is the case, it will be very tough to do since the daq 6009 does not support hardware timing. In this way, all the timing will have to be done in LabVIEW which is software timing and as such is not as reliable as hardware timing. For this you will need a data acquisition device that supports hardware timing with counters. You would need to configure two counters for the clock lines and a third DIO for the serial data line.
Robert B
RF Product Support Engineer
National Instruments