I can try to help you out on some of these:
1. I'm not sure what you mean with this one. You can build an array with the waveforms and pass them to a chart to plot all three at the same time.
2. The digital indicator is a tough one to troubleshoot. Make sure that the values you are reading from the file are correct ( 1 or 0 ).
3. If you are using the Open/Create/Replace File VI, you can set the advisory dialog to False. This way, it will not keep asking you if you want to rewrite the file. In order to keep it from asking for the file name, just pass in a constant for the path name instead of leaving it unwired.
J.R. Allen