Oh I forgot to mention, EVAP purge and switch weren't included with the new engine so I kept those attached. Could a vacuum issue also cause the knock in a single cylinder?
EDIT: I swapped injectors 3 and 4 over, thinking it may have been an injector problem, but the knock didn't travel with the injector and injector 4 still shows a knock and I'm still getting smoke from the middle rear of the engine... :-\