Jochen,
Thanks a lot for you feed back. I definately need to go faster than 1-4Khz. I am going to experiment a little with the idea of using the output signal of one of the encoder channels as a clock. I'm not real familiar with using external clocks to trigger reads on the NI-DAQ 6036E. Also the motion controller is FW-7344 used with MID-7654.
I guess I will try to look at the examples and get some ideas, unless you have an example yourself that you think would be helpful.
Thanks Again
Wes