Hey,
It sounds like there are two parts to your problem: the first is that you need all of your measurments synchronized, and the second is that you need to add timestamps to them.
For synchronization, you just need to make sure that you start all of your acquisition at the same time, and that everything is using the same clock from your PXI chassis's backplane. Your FlexRIO can access the triggering and clock lines on your PXI chassis directly.
For the timestamp issue, the easiest way is probably to have your real-time controller timestamp when all of the acquisitions start, giving you the timestamp of your first sample. Then, from your sampling rate, you can calculate the timestamp of each subsequent sample as they come in on your FIFOs. Here is an example of someone doing something similar on a cRIO.
FPGA Timestamp Sync
https://decibel.ni.com/content/docs/DOC-23030
Britton C.
Senior Software Engineer
National Instruments