That detonation at shutdown you speak of is called "run on", that typically happens when the throttle blades are open too much over exposing the idle transfer slots giving the engine extra fuel.
If everything was set perfectly before, sounds like the primary throttle shaft is sticking and the return springs are not strong enough on its own to set it back to the actual idle you set, take the carburator off and spray carb cleaner into both throttle shafts just to be sure.
I currently run the same Holley 670SA on my ZZ4 crate engine, but its the earlier version with the idle mixture screws on the primary side metering block only, its a decent carburetor once you've figured out all the bugs, lots of complaints over that one and the Holley 770SA, of which i also have thats the earlier version as well, it came with the car, the engine seems to be much happier with that one, you're 406 would benefit IMO with a Holley 750, vacsec for auto, mechsec for manual transmissions.