I do notice on the plots of daily power that the PV power shows shoulder at the beginning and end of the day.  Where does that come from?

The problem is that HOMER assumes you are entering global horizontal radiation in the Solar Resource Inputs window, so it resolves it into its direct and diffuse components (using the Erbs model) before it does any other calculations.  If you could turn that feature off, you could enter DNI directly and everything would work correctly, but unfortunately HOMER does not currently let you turn that feature off.