I have a very similar question here: http://forums.ni.com/ni/board/message?board.id=40&message.id=2630
I ended up figuring it out today. It's really simple. I went analog in to AIn14 and AIn15 which were free. Then the program does a multichannel scan of the signals (collects array of 2 waveforms), call them Signal 1 and Signal 2 at some scan rate, I used 100,000 S/s for 10,000 samples. Then I split the array into two separate waveforms. Then I did an edge detect on each one and it returns the position in the array where the falling edge occurs. The difference is the delay (after correcting for the scan rate), unless Sig2 comes first in which case the delay is the period - (or +) the difference
To find the period I used a subset of the Signal 1 waveform from the first falling edge on to the end of the waveform, then did the same edge detect except set the reset setting to true instead of false so it wouldn't detect the low signal which was now at the position 0 in the waveform. So it would ignore the initial low value, wait for it to go high, then detect the falling edge position.
Anyway, it works awesome, seems very accurate and gives very stable readings.