For what its worth, if I were putting a 7.3 glow plug controller on a 6.9, I would not locate it in the factory position anyway. It's much better off on the bracket that Hypermax sells, which moves the controller to the drivers side valve cover area. This is so any turbo project will not interfere, and the controller can be relocated there with no changes to the wiring.
If your moving a 7.3 pump and lines to a 6.9, technically the lines are too short, but they will fit just the same with no operational difficulties. Just be sure to move the timing adapter along with the lines. If you have the option, switch all your lines over to the 6.9 style and ditch the adapter when bolting up to a 6.9.