I removed all the Kexts w/ *USB* and replaced w/ kexts from 10.10.5
drwxr-xr-x 3 root wheel 102 Aug 22 16:23 AppleMIDIUSBDriver.plugin
drwxr-xr-x 3 root wheel 102 Sep 16 18:14 AppleOSXUSBNCM.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 AppleUSBAudio.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 AppleUSBDisplays.kext
drwxr-xr-x 3 root wheel 102 Sep 22 11:01 AppleUSBEthernetHost.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 AppleUSBMultitouch.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 AppleUSBTopCase.kext
drwxr-xr-x@ 3 root wheel 102 Jul 30 2012 CalDigitUSBxHCI.kext
drwxr-xr-x@ 3 root wheel 102 Jul 30 2012 CalDigitFastIO.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 IOUSBAttachedSCSI.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 IOUSBFamily.kext
drwxr-xr-x 3 root wheel 102 Sep 19 2014 IOUSBMassStorageClass.kext
This not only resolved my USB3 issues on my Asus ROG w a FL1000 USB adapter but also fixed sleep/resume issues.
Everytime I update the OS I keep a backup of the SLE folder in case something breaks so I can easily rollback the kexts.
I use the latest Clover.
I've also rolled back the Wifi and bluetooth and AppleHDA drivers to get airdrop and sound to work properly. All my hardware is recognized and working properly.
I'll be updating to 10.11.2 tonight since NVIDIA finally released the 10.11.2 official drivers and see if can apply the same rollbacks to get everything to work properly.
I check if all the replaced kexts are ok/properly matched after I update the SLE folder and the caches are rebuilt
There's a couple kexts I not listed above but that are revealed when you check the syslogs.
I tried that but the model of the FrescoLogic card that is built into the older ASUS ROG's G53/73 is not compatible w/ the FL1009 drivers. CalDigit drivers seems to work fine.
It was a hassle to rollback all the relevant kexts but everything seems to work perfectly now in El Capitan just like when I was in 10.10.5.