I did notice now that the USB is functioning correctly, sleep is no longer working (which doesn't surprise me).
I was getting this in the log: Wake reason: EH01 EH02 XHC HDEF
Which lead me to here:
http://www.insanelymac.com/forum/to...-usb-series-89-keeping-vanilla-sle/?p=2177035
And I tried the same steps as described (previously renamed EHCx, applied usb 15 limit patch to clover, and patched DSDT with that "ACPI disconnect from PCIe identity") and that improved things a little, in that the wake reason is a little more specific:
Wake reason: EH02
[IOBluetoothHostControllerUSBTransport][SetRemoteWakeUp] -- deviceRequest() failed: 0xE0005000 (kUSBHostReturnPipeStalled)
ARPT: 79.039742: AirPort_Brcm43xx:
owerChange: System Wake - Full Wake/ Dark Wake / Maintenance wake
Going to try and hopefully resolve. Any suggest appreciated as always