Re: the “hole on the mushroom thing” (air filter)… on the Perkins 4107 (mine still runs great,too) there is (or should be) a short hose just under the “cap” of the “mushroom” going from there to the valve cover. This is for crankcase ventilation and has nothing to do with getting air to the engine for combustion of the diesel fuel. If this hose is missing it’s no big deal as the crankcase will still get the required ventilation.
Fred “Oasis” #99