Hi dennyz,
to answer your questions.
1. You can use your PFI-ports for triggering. Please have a look at "Cont Acq&Graph Voltage-Ext Clk.vi" or "Cont Acq&Graph Voltage-Ext Clk-Dig Start.vi" that are shipped with your LabVIEW installation. It doesn't matter where the triggering signal comes from.
2. If you generate a trigger signal from one device and use this on both, you use the same time base. You cannot synchronize the clocks on both devices, but you can generate a trigger for both.
3. As you don't need the for loop in your implementation, as you mentioned with "Indexarray", you should use this. Try to use as less loops as possible.
4. As you read waveform data, you don't need to create an extra timestamp. When you trigger the measurement with one trigger signal, you have the same time base.
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