first of all i wanna thank all contributors for their work. helped me a lot to figure out my usb problems. after 3 days i finally got most of my usb-ports working on an GA-Z87X-D3H.
There still are some things i don't understand yet, but i have little time at the moment. Writing again soon.
But, there is one thing which comes to my mind because a lot of customers have problems with Skylake and Win 7 (working as it-supporter).
Intel has dropped EHCI support in their new chips. A good reference is the data sheet for the 100er series (chapter 34):
Maybe Apple changed the USB subsystem because of upcoming Skylake-Macs. Maybe there is some useful information in there.
For Windows 7, USB is not working during installation oob. You have to patch your installation media or change some BIOS settings (depending on board manufacturer).