I believe that the rope scars are from a hanging where Norrington stood with Jack on the scaffold instead of behind. I'd like to think that James decided to join Sparrow, and under pain of death would not leave his side. I think they were brave and strong and held hands as the floor went out from under them, the ropes digging into their necks. And I'm hoping that love and friendship prevails and they somehow manage to escape. Maybe the ropes broke suddenly or William flung his sword and cut them, and maybe they both fell over the side of a fortress into an angry sea and were never seen again. Now they are older, wiser, still in love and they lived happily ever after.