How do I match up the pins specified in the DAQ-STC Technical Reference Manual with the actual pins on the CB68-LP break-out board that connects to the PCI-6035E via the ribbon cable? I want to trigger an interrupt by setting a signal on IRQ_IN0 (specified in Appendix C of the DAQ-STC manual), but no such input exists on the CB68-LP.
That is because no such pin exists on the connector to the DAQ device. The DAQ-STC Reference Manual is a reference for the DAQ-STC ASIC. The pins referred to are on that ASIC. See your E-series User Manual for the pins available on the IO connector of your DAQ device. These will match the CB68-LP pin-for-pin.