Hi J_K,
You should be able to use Pattern Input with you PCI-6534 (synchronous timing). The key is to use your pulse as a trigger and the ReadEnb signal as your external clock.
Therefore the pinout you would use is have your interrupt signal to STARTTRIG to start your operation and then tie your ReadEnb signal to REQ signal. You would also need to specify in software that you are using an external clock signal. Hope that helps.
Ron