It sounds like you're wanting to different applications? In this case, you could have to VIs running. They could have a global array which can pass data between the two of them. You could also have the timing.vi write the data to an file and then your main.vi read from the file, but there's a bit more overhead associated with that approach.
As far as being affected by the PC system, there is no way around this, assuming you are running on Windows. Unless you have a real-time system, you can't get around the overhead of Windows. It has to share resources with other applications all the time.
J.R. Allen