Ok so after much experimentation, exporting it as an fbx then reimporting it into a new scene seemed to have fixed the issue to an extent.

Still though, that's kind of hokey and I'm still not sure why the original blender scene would hate the shoulder bones in the first place.

Honestly, the older version of the blender smd tools never gave me anything close to this issue before.

Anyone got ideas? I think there must be some setting or index ticked, I just can't figure it out.

experimented a bit, seems deleting the shoulder bones will get it to export, but I kinda need those bones. Why is this happening?

https://puu.sh/E6HCW/e000406baf.png

I also get this issue when I uncheck the collections for some of the characters in order to export their chibi and dolly versions. Does this new version seem to hate blender 2.80's use of collections instead of layers or something?

https://puu.sh/E6Hnt/f5eeb07d2c.png

I can't seem to export a model in this newfangled version of blender source tools in blender 2.80.

It seems to hate the clavicle bone. The older versions were much simpler and straight to the point. What can be done to solve this issue? I was able to export a different model that had the same bone names and all earlier.