This is unfortunately a case for the lesser of two evils.
One approach would be to weld up the faces that are over lapping, apply a chequer texture to it and move some of the other verts around to minimise the distortion.
The other would be to detach the faces that are least likely to show a noticeable seem and just deal with it in photoshop which would probably the way I would tackle it.
hope that helps
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