Unfortuantely, it's not really feasable at this point. I sorta left out a step.

When I use Photoshop, the skins are painted in Photoshop, then the textures are imported into a 3d modelling program, then they're applied to the 3d model. Then the 3d model frames are rendered out and organized into strips, which then go to Carla, so that she can go insane trying to align them all. (just ask her!) The source Villager files are 3d models, and the clothes are essentially part of the 3d model, so it's hard to separate the two without going back to the source files. I suppose it's possible to render out the outfit minus the extremities, but it'd take a loooooot of time, and then there'd be all sorts of other issues with masking, deleting geometry, etc, lots of technical boring 3d rendering stuff. ;-)