A few comments:
1. It isn't clear what exact measurements you intend. I haven't done photodiode measurements but have been in numerous related threads here and such measurements are usually done with counters rather than "regular" digital acquisition
2. You use the term "correlated digital" which is a term typically reserved for M-series (62xx) devices which didn't have their own internal timing engine available for acquisition. Your X-series (63xx) devices do have an internal timing engine for digital, so you wouldn't need to limit yourself to "correlated digital". However, also, you'll probably want to use counter tasks rather than digital anyway as previously stated in #1 above.
3. You can use external connections of timing signals to PFI0 (or another PFI terminal...) on both devices to help with sync. The exact kinds of connections and config will depend on the exact measurements you're doing and the nature of the sync you need.
4. In the longer run, it can be handy to connect the 2 PCIe devices *internally* with a RTSI cable, allowing the devices to share various timing signals without the need for external wiring.
-Kevin P
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