@odenhail
This post is over 2 years old...you should make new thread for Mojave.
You don't need to replace AppleHDA.kext. You should keep it vanilla.
Add Lilu.kext + AppleALC.kext to clover kext folder, change layout-id to 12 in Config file and DSDT if appropriate.
Add CodecCommander.kext to /L/E if you're having noise issue in headphone.