Charles,
Your application is not totally clear, and may need some more detail for a totally correct answer. I would recomend submitting this to NI's Email support team at www.ni.com/ask. I do have one recomendation you can look into first.
You could configure a port to do Pattern Generation input that is triggered off of the StartTrigger. In your read loop, wait for the trigger. The first time through the loop, don't read any data, just wait on the trigger. You would have a case statement, that would allow you, on the second interation of the loop, to ouput your high and low pulses on a second port and then change the number of data points to read. I have included a small snipet that may help you understand what I am talking about.
Nick Wilson
Applicaiton Engi
neering
National Instruments
www.ni.com/ask