It seems like you need to give more thought to your program architecture. A good measurement application must be written to handle signal loss gracefully. The fact that your acquisition rate changes based on an error condition leads me to believe that you are using software timing instead of hardware timing. You've got two super-powered pieces of hardware in the 4472 and 6602. Let them be your timing sources. Acquisition rate (or scan rate) does not change when you set it in hardware.
All these things come with experience. You may benefit greatly by hiring an Alliance Member to get you past the initial hurdle. We do this stuff every day.
Daniel L. Press
PrimeTest Corp.
www.primetest.com