Might be in the UV map believe it or not. Just as an experiment subdivide the welded mesh and have a look again. I just encountered some weird dark artifacts on a figure I'm working on. Wasn't any kind of polygonal issue, turned out to be an artifact at a spot on the UV map where a cut stopped and edges flowed into 2 wings of the symmetrical chart. I fixed it by extending the seam cut up a couple of polys. Subdividing also seemed to help but the mesh was already at a final level of division so it wasn't really a fix option. The artifact looked like a dark grey bruise. Of course it could be something else but just pointing out that it's a possibility.

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