Hi Bennett,
Thanks for looking in, I've kind of stuck this one on the back burner but there are still issues.
I have had great issue with cutting models up and not getting normal lighting irregularities, or problems with skinning.
As example my biggest problem is detaching a head from a body, I tried various methods of manually fixing the lighting at the seam before export to no avail. I've tried to make the skin work as best I can but some extreme movement of joints will cause minute misalignment in vertices.
On export trying pretty much all variations of single commands to join the head and torso result in either complete incorrect stitching of the object together or some minor lighting issues still.
The last command I used was some crazy stab at everything and seems to give the best result for these 2 meshes.
fixseam.exe /E .001 Torso.hgm Head.hgm /O /I
As you can see in the pic there is still some visible stitch to the seam but they seem fairly well glued together apart from tiny visible gaps at extreme movement noticeable at close distance.
I am basically hacking this guy together myself though, I do hope to have someone more capable get on board to polish off issues like this so it's not a pressing issue right now.
Also as such I'm still unsure how much the model is to blame itself.
As far as fixing seams, forgetting any skinning issues, I can not get the tool to fix all welding and lighting errors.
Most command attempts end up with the meshes totally off causing most of the throat to stitch to the neck.
Any help would be much appreciated though, I would gladly look at it again if anyone can suggest a solution.

Edit: Also to add, I'm currently not even running the hands through the tool, for some reason I was able to "fix" those normals before export and as they're not split at the wrist they work fine anyway.