I don't see any obvious problems, but I do have a number of suggestions.
Your CAN/DAQ-RTSIconfig.vi uses the DAQ card as the master for the RTSI sync signal. Try switching it to use the CANcard as the master. The CAN vi's are probably slower than your analog in VI's, so you want to use the slower of the 2 to syncronize. (that will mean you need bigger buffers for the analog input VI's)
Along that same idea, have you tried changing the DAQ scan/Update rate? It was set at 500, so your analog is scanning at 500 Hz, but you CAN is only doing a read every 10 mSec.
Try increasing the CAN read queue length. Some faster apps need 200 or 300 for a buffer
Move all non-essential VIs out of the main loop. Try rewirting the VI to do ONLY CAN & DAQ readings in the m
ain loop, and pass the reading to an array. When you stop the aquisition, then you can format the array into strings and write it to a file. If you can't do that, al least try moving the string formatting parts outside your aquisition loop.
Delete the graph and indicator from the front panel, or at least move it out of your main loop. The CPU loading to redraw the screen may not seem like much but it can slow you down.
