I am almost reluctant to suggest you look into this, because it was such a dumb thing, but I found that my built in 3.0 USB was still working after upgrading to Sierra, but that the ports in my case were not working anymore. It was not the DSDT or a kext, or anything like that. While doing other things related to the upgrade (probably installing the new NVIDIA 1070 that was the proximate cause of the upgrade) I had pulled the cable that connects the Motherboard to the case USB 3.0 ports. oops. Putting it back in fixed the problem