I will make another guess. You have 4 blue-insulator USB connectors and 2 black-insulator USB connectors on your rear panel (motherboard), plus the 2 black-insulator USB connectors on your front panel (as you wrote). So, if that's right, your USB connector configuration matches mine even though your Z97-HD3 is different from my GA-H87N-WIFI. So
my Hackintool display (after mapping) looks like the image below:
View attachment 562713
For my computer, my 4 rear-panel USB2/3 "blue" connectors have HS03-HS06 names for the 0x03 thru 0x06 ports, and they are also carry the SS03-SS06 names at 0x12 thru 0x15 ports. My 2 rear "black" USB2 connectors are named HS07 and HS08 at ports 0x07 and 0x08, and my 2 front "black" USB2 connectors are named HS09 and HS10 at ports 0x09 and 0x0A. As you can see, HS11 is an internal port looking like a USB1.1, at port 0x08. (Note that Hackintool "thinks" all my connectors are USB2/3, although not true.)
Although your USB connector locations, both "blue" and "black," are physically identical to mine, I have no idea how your HS and SS names are arranged. Your current USBPorts.kext info.plist is confusing to me. I would expect 4 USB2/3 ports, 4 USB2 ports, and a few internal ports.
Instead, I see 3 USB2/3 ports (HS01, HS02, HS09). 2 USB2 ports (HS05, HS06), and 6 Internal ports (HS07, HS08, HS11, HS12, HS13, and HS14), plus the 4 SS ports (SS01-SS04) which I would expect.
Would it be possible for you to use Hackintool (again?) to map your ports and upload a Hackintool image such as the one I just posted? Maybe that would point out the apparent discrepancies. If so, your USBPorts.kext info.plist could be edited to clear that up. (You would have to boot, open Hackintool, "sweep" the USB page of Hackintool with the broom and then click the arrowed-circle at bottom of the page, before starting mapping.)