I think I ought to clear up some confusion here. Scanning the analog inputs of the 6023E board does not use up counter 0 and 1. The board has reserved timers for this purpose. You can use counters 0 and 1 at the same time an analog acquisition is taking place if you want.
Also, the maximum number of samples you can acquire probably needs some clarification. In the NI-DAQ Function Reference Manual the SCAN_Start() function mentions the 2^24 limitation on the size of count. So yes, for a finite acquisition there is a limit. However, if it is a double buffered (ie. continuous) acquisition "count" is just the size of the buffer. You can actually acquire an infinite number of samples.
Now addressing another issue... You should have no problem acquiring the a
nalog data at that rate. However, the digital port on the 6023E does not support "stobed" or "clocked" I/O. These lines support only static, software-timed read/writes. For this sort of operation, you will need a 650x or 653x series board in addition to your 6023E. Alternatively, you could use the 6025E board which contains digital lines with the same functionality as the 650x boards.
I hope this helps!
Russell
Applications Engineer
National Instruments
http://www.ni.com/support