Alex
When using a Start and Stop trigger with Pattern I/O using the PCI-6534 device, it does not work as one may think. It starts reading in data into a circular buffer when the start trigger comes in. The data will continually overwrite itself in the buffer until the Stop trigger comes in.
When the Stop trigger comes in it keeps x amount of data from the cirular buffer and then aquires x amount of posttrigger data.
Since you have an undetermined amount of data to acquire, the best solution I can think of is to use a counter either on an E-Series board or a NI 660x board to generate the clock. You can start this clock from a start trigger and stop it on a stop trigger. There is already an example that does this that I have attached below.
Brian