Hi, I looked at the ELVIS Hardware User Manual and noticed that you have 12 channels that can be used as differential, Reference single ended or non reference single ended. Unless you have them all busy I don't see why you can't use the analog inputs. About the sampling rate, it will be determine by the M Series DAQ device that you are using and the source of the signal. It is a good practice to sample, at least, 10 times faster than the frequency of the input signal. The documentation of the card should show what the maximum sampling rate is.
Now, Open the example called "Multi-Device Synch-Analog Input-Cont Acquisition.vi" at the NI Example Finder under Hardware Input and Output»DAQmx»Synchronization»Multi-Device. If you get the same results shown in the picture then you need to analyze if the voltage divider is affecting the phase.
For more information about synchronization check the article called "Synchronization Explained".
Good luck!
Alejandro C. | National Instruments