Are you familiar creating virtual channels in MAX? If 16 channels is your limit, I think virtual channels would be good for what you want to do. You can use the EasyI/O functions (CVI/LabWindows) to acquire the data from your virtual channels. Assuming that you will use a software timer for you acquisition function, you might create a variable equal to the time interval of your software timer. Create another variable to increment itself + the time interval variable.
t_stamp += interval;
You can write your time stamp data to disk with each clock cycle along with your AI data.