Ive had my MBN cat single turbo for 17yrs. Had this issue more than once with the thumping at the air cleaner assembly. Its actually very simple to diagnose. Use a stethoscope you can get at Harbor Freight fairly cheap. Listen to each exhaust port at the manifold. Listen for the thumping and align it with the culprit cylinder. Its either a bad injector or a bad intake rocker on that cylinder. Over the years Ive had to replace an injector on one cylinder and an intake rocker on another. When inspecting the intake rocker, check the button. The button is held on by an oring and pivots on a stud that wears out giving the intake a huge amount of valve lash which allows you to hear the thumping. If your out on the highway and need to get home, just take the valve lash out of the culprit rocker and it should smooth out but vibrate slightly. it will run and should get you home. Over time, the injectors can mess up too. The oring on the lower side of the injector hardens from the heat and breaks apart allowing more fuel into the cylinder than usual. Check your return check valve on the secondary filter housing for small pieces of oring..