You can make a frequency measure with only one counter. This method use
the internal timebase as source and your input signal as gate: the
process take the number of clock period in a period of your input to
compute it's frequency.
Accuracy of this method is quite good if the input frequency is small
compare to the internal timebase. So with the sensor you described:
6000rpm => 100 rotary per second
with 120 top per rotary => 12000 top per second
The AI-16E-4 use a 20MH internal timebase, so I think there is no problem
More information about
frequency measurement...
For the synchornisation, I'm not sure to clearly understand what you
need, but take a look to the DAQmx timming and DAQmx start trigger VIs.