[Solved]
My Sierra installation was an upgrade not a fresh install. As a result I updated Clover to the latest version but retained my original config.plist file. The solution was to edit the config.plist file with the following changes:
Under <key>Intel</key> I changed true to false
Under <key>KextsToPatch</key> I removed all <dict> .... </dict> entries. These modified the AppleHDA for the realtek chipset.
In the EFI folder for kexts/10.12 I removed the realtekALC.kext I had originally copied to this location prior to the system upgrade.
I believe the only step necessary was to remove the entries under KextsToPatch but all information is included for completeness. I also have the built in GPU disabled in CMOS..
Hope this helps someone.