Very cool man. Something that is very useful is the ability to transfer only selected area of the mesh. This is particularly useful for shape keys for animation from sculpts for generating normal maps, displacement maps, AO, etc. They also have this feature in ZBrush and Mud Box. I was wondering if you could add that ability also. They use masking to do their partial sculpt transfer. The code for transferring a selection to other models based on point position already exists in Blender while in edit mode on a mesh you hit the W-Key and then the specials menu comes up and then select Blend From Shape. You can choose what shape you want to blend the vertex positions from, and control the amount of blend with the mouse. There's also 'Propagate to All Shapes' which takes the current selection, and pushes those positions though, updating all other shapes.
I wrote a python script that lets you transfer point positions based on a selection from one model to another if that would be useful to you. http://blenderartists.org/forum/showthread.php?t=131404
Seems like your project is well setup for layer sculpting where you can sculpt on a layer like in photoshop or the gimp and then turn this layer on or off. Also if you could have it setup to have a slider for 0-100 percent the layer sculpt is expressed on the model that would be really cool. They also have this feature in ZBrush. The way you have done your project is super cool and it seems like you are really setup to do something like this.
Oh and to speed it up voxels seem to work very well for this because ZBrush and Mudbox are using them for the sculpting and ZBrush is also using them for painting. I know voxels are being implemented into Blender for effects, but I also know of an open source project that has voxels for geometry. Hopefully it is useful to you. I have no idea what method you are considering right now for the sculpting.
Your doing awesome work. Best of luck and I can’t wait to see the final results. I hope this information helps you if even a little bit.