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Merging a bunch of meshes into a solid mesh, manifold mesh?

I've got a bunch of photogrammetry scans I made using Autodesk ReMake. I have put them together in a scene in Blender. I have built up some additional meshes around this composition to fill up the bottom so it's not just a bunch of flat planes overlaying one another. I am trying to merge everything together into a single mesh, so that I then reproject all the texture and normal map information from the higher poly seperate meshes into the the single lower poly mesh. That way it's not just a bunch of random scanned meshes but is all a single coherent mesh but still has the old diffuse map color information mapped to the new uv. 

I know how to do the reprojection of textures. I'm using marmoset. It's easy. The problem I'm having is how to get the meshes to all bind. 

I've tried MeshMixer (it gets very comfused) , zBrush zremesher (that kind of works but I loose a lot of detail), dynamesh (doesn't work gets all glitchy looking), and MeshLab. Any advice on techniques I'm not aware of or should try? 

I'm also going to try using Instant Remesh, but it usually can't handle stuff of this high of poly for some reason. 
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