Hey zedtremont, did u try tri-planar projection? Basically for each fill layer you have (even for the masks) you have an option to either use UV projection or Tri-planar projection. If you use the latter on EVERY layer in one texture set and then add (or copy) the material from this first texture set to another texture set, both textures would be perfectly aligned automatically. You would have to tweak in two places at once if you want to add any changes later though, so your suggestion is 1000% valid, but as a temporary solution do try my method.