Hi Dustin,
Did you see the KB about cRIO CAN Sync? Here is the Link again. It explains that the CAN timestamping starts on CAN "Start" and has a resolution of 100 ns. You could measure the timing offset to your DAQ process and simply remove this offset ones, as described within the KB.
KB LINK
The same is true for multiple channels from multiple messages. If they need to have the same timestamp, you could allign the timestamp for all messages to the timestamp from the first message.
DirkW
