I took the running boards off to paint, and everyone agrees that the Ranger/Super cab looks better/cleaner without them... As do I... I'll keep them off for awhile and see if it grows on me.
Call me crazy, but the pinch welds on the lower sides bugged me, so tonight I taped them off and sprayed them satin black. Added a finished edge... before and after pictures.
Cardboard is more than adequate to protect the paint, I would not put my new truck in harms way, the bike locks in and doesn't move at all, but a quick bungee does add a bit more security.