Sort out a complex UV map for a complex mesh I asked a question yesterday regarding texturing, and now I've gone through the work of unwrapping parts of the mesh and texturing them separately. It looks beautiful.



I now have the problem of a UV map that is kind of a mess. Several textures are used, and each is derived from its own image. The exception is a texture image that was generated with photogrammetry software, which is a composite of image textures.



Now when I look at the UV map it is a huge mess with overlapping islands, though referenced to different images. I've tried to bring it into other software (Meshlab and Mudbox) and I get texture errors. Is there a way to easily sort this based on image assignment? Alternatively, is there a way to automatically generate a separate and single texture file of combined images?

I've attempted to bake textures with no success--granted I have no idea what I'm doing.
Select all the UVs in UV/Image Editor, from the UVs menu select UVs From Islands. 



Then in Object Data tab create a new UV Map and unwrap the model. While all the UVs are selected, create an image in the new UV Map where the new texture will be baked and keep this UVMap selected.



Then make sure you have a material and the original texture is applied there using original UVMap.

 

Click on Render tab and in bake menu select textures and click Bake button.



In the same way as described, it is possible to bake multiple materials that are using same or different UV Maps, to a new single or multiple UV Maps, each with separate texture.

The described above steps are aplicable for Blender Render internal engine. Workflow for Cycles is a bit more tricky though is well depicted here:
Possible to bake texture to new UV map?