After changing the thermostat housing on my 4.0L, I now notice a thumping sound like a hand on an upside down empty 5 gallon plastic bucket when idling..... it's only every minute or so.

Air in the system?

 

Welcome to the forum

Yes, most likely
When refilling cooling system always take one heater hose off at the firewall to let the air out of the engine side of thermostat

Also REVERSE the heater hoses at the firewall every 2 years when coolant is changed, or anytime when doing engine work
It will help heater core last longer
Heater cores have no direction of flow, reversing the hoses "back flushss" the heater core while you drive