If your only problem is loop iteration times, then I would recommend splitting up this process (acquisition and analysis) into two parallel loops. This way you can have one loop dedicated to acquiring data quickly and pass the data to the other loop that would analyze the data accordingly.
An application design pattern along
these lines might help you get started. Also look into other design patterns such as the
Producer Consumer that transfer buffered data from one loop to the other using Queues. Hope this helps!
Jarrod S.
National Instruments