With the 6009, you actually have a very difficult task. The digital I/O is software timed only and it has no trigger capability. It does not have a counter output so you can't use that for a pulse train either. In order to detect the signal, you will have to do a continuous read, then output the pulse train bit by bit. The timing for this would probably be no more than 1kHz. A software delay of 80ns is just unreasonable on windows. With the amount of jitter on a non-deterministic OS, you might be able to achieve something in the msec range.
A different DAQ card is almost certainly called for.