mpsarma1,
If you would like to output pulses with specfic characteristics I would recommend using counters for this task. With that said, the digital I/O of your board is software timed and may not be as accurate as you may need. I would suggest looking at the example Gen Dig Pulse.vi (used for counters) and Write Dig Chan.vi (Used for outputing on digital lines) under Help>>Find Examples. I have included an example which demonstrates how to generate a pulse on a digital line. It is apparent that this will not be accurate (ms range), though. To be more precise for both the counter and digital lines, an external trigger an be used to control the time for which the pulses are output.
In terms of finding the period between two pulses on different lines, you would want to use a buffered period measurement. Buffered period measurement would only require one counter, though. You would tie the 80MHz timebase to the source of the counter, use one of the pulse lines as the gate and the other as an arm start trigger. This will allow you to get the time from the trigger to the gated pulse. I have attached some documentation which explains Arm Start and other counter applications a bit more.
