Looks like you know how to use MATLAB. About all I might offer is to use the 'Color' option in plot to specify specific colors. Or you can look at colororder to set up a sequence of default colors to use if you don't use the color option.
If you want different linestyles, I'd plot them separately:
% Plot Y vs. X with one linestyle.
plot(X([1:42]),Y([1:42]), 'Color', 'r', 'Linestyle', '-.', 'linewidth', 1.0); % first linestyle
hold on; % Don't blow away prior plot.
% Plot Z vs. X with a different color and linestyle.
plot(X([1:42]),Z([1:42]), 'Color', 'b', 'Linestyle', '--', 'linewidth', 2.0); % Different linestyle
help colororder
