Hm, so originally I did use the x99.zip file and your patched dsdt but had the audio issues, which is when I started looking for other builds with this board. The one from the x99 build guide (with the asus.aml file) did fix the audio issue.
For testing I've swapped back to your dsdt and the x99.zip and the audio now detects all devices and plays back (initially it it only detect the z-cinema speakers, no onboard, hdmi audio etc). However still having issues with the audio input from the CI1 usb interface.
Actually the playback from the ci1 doesnt work as well, similar issue to what I had initially where the app just hangs. All other devices are functioning correctly.