Tim,
If you're going to be working with a TTL-compatible pulse train, the most straightforward solution is to use the hw counter/timers available on the multifunction boards. I've done some apps with a similar carrier freq and the good news is that you can get a reasonable quantization error on your measurements -- 1 part in 10k-20k, which is better than the 1 part in 4k you'd get from a 12 bit analog measurement.
The data acquisition should be done with a counter timer programmed for buffered period or frequency measurement. Under DAQmx, you'd use a DAQmx Timing vi set for "Implicit" to let the pulse train edges act as a variable-frequency sampling clock. You may also need to use a DAQmx property node to specify the appropriate timebase -- on E series you'd want the 20 MHz rather than the 100 kHz. Then the intervals you measure will count ~10k - 20k timebase cycles per cycle of your external pulse train, leading to a fairly low quantization error.
Post back if you need more info on using counter/timers. In the future, you might want to put signal and hw related questions in one of the hw boards. It's probably more likely to get answered sooner.
-Kevin P
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