Yes, you can make the graph any size you want. You need to (1) wire the desired dimensions to the "Plot multi XY" terminal and (2) make the picture indicator the correct size. Attached is an example with 400x400.
A waveform graph needs all traces the same length but in your case some a zero length if they are not displayed. Instead you can use an XY graph and feed it directly with the cluster output from the small FOR loop.
To keep the current settings:
(1) If you call the same VI multiple times within the same run, the settings are retained (just don't reset them with a local variable as you did in the stop event case).
(2) If you want to have certain traces checked by default when you first run it, edit the VI, select the desired traces, then right click on the boolean array "data operations...make current values default". Now save the VI.