AppleALC.kext should be where Lilu.kext is to run, so move it to Clover /kexts/Other folder.
To change the layout-id, you have 2 places to check.
1) Config file / under Devices->Audio->Inject. Enter the # 12
2) DSDT, you'll need an app like MacIASL to open the file. Search for HDEF, look for layout-id, change it there.Or best to just remove the layout-id declaration