mmv,
The digital lines on the 6601 are static, so you will only be able to time them using software, which is non-deterministic and can't be accurately timed past about 1kHz (depending upon the computer and the operating system). The counters are fast enough, but the only options you'll have would be to set frequency or pulse width, and it'll have to be a repeating pulse train.
Your best option is to purchase one of our motion controller cards that is designed for use with this type of application.
Elijah Kerry
NI Director, Software Community