Thanks for sharing with us your plans on your console, sounds very interesting!
For your question, I should think you would want to preserve the original Galanti organ functionality. If that is the case, the stops may already be midified and can work with Hauptwerk (I believe the manuals and pedals at least already are midified on current Galanti's). You may not be able to add a new manual and stops to the existing hardware, but you may be able to add them to a separate Midi board that Hauptwerk can recognize. This has the benefit of preserving the original functionality. The hardest part would be getting Hauptwerk to play through the existing speakers, but if you have a professional doing the work for you they may be able to do it (you could have a switch that switches from Galanti input to the PC input to the speakers.) The speakers would need rewiring to work this way. A small computer like a Mac mini might be able to be secreted away in the interior. Surely others have good advice for how you could proceed as well.