I was struggling to get all my USB-3 ports running on the right speed and get rid of the portlimit patch.
Now I have it perfectly working and running on 10.12.3.
In my attachment I have the kext files, clover config files en SSDT for USB and the BIOS settings for F23C.
Remove any previous versions of USB injectors and SSDT files.
Install the kext in S/L/E
Use my config file for DSDT edits for EHCI and XHC
Use the BIOS settings as in my screenshots
And you should be good to go.
No need for port limit patch and waste unused ports and power.
Big thanks and credit goes to RehabMan. He made the kext and how-to.
I just did the job on my system.
I was thinking to share this because I know you are never alone with an issue. :-)