All very interesting...
I think the best rod to use would be the stock Roadholder rod, since it situates perfectly in the tube already and should be an appropriate length...shouldn't be hard to put a cupped cap on them, and a top-out spring, if needed, would be easily retained between that cup and the retaining nut on the bottom of the stanchion.
The right height for the rod cup would be essential, given the possibility of interference between the underside of the rod cup and the stanchion bottom nut. The stock arrangement fits completely through the hole, so that's not an issue...I really don't know how everything sits at rest and at full compression, but could start measuring to see...
I'm not sure I follow you on replacing the shuttle valve. What would the purpose be, and how would it allow the valve emulator to sit where it needs to? The normal shuttle valve damper rod is a main reason you can't put a valve emulator in.
Edit: also, with the goldwing forks, is the bottom-out cone you mention a hydraulic function, or is it a physical bumper as on a rear shock?