I am not very good at written communication, but will try to answer some of your questions. The 53 series Detroit diesel is a 2 cycle engine. It has no intake valves, may have 2 or 4 exhaust valves per cylinder depending on set up. The cylinder sleeves have port holes at the bottom of the sleeve, the sleeves are surrounded by an air chamber in the block, this area for air is called the air box. The blower is simply a vane type air pump, 2 roller, 6 lobe, to pump air under pressure to the air box. Being a two cycle engine , the strokes are compression and power.To provide intake and exhaust the blower does the work. As the power stroke pushes the piston down, at the bottom of the piston travel, the port holes in the sleeves are uncovered, and the cam and valve train open the exhaust valves. Pressure air from the blower in the air box forces air through the cylinder and out the exhaust valves to purge the cylinder. As the piston reaches the bottom of the stroke the ext. valves close, and the blower forces air into the cylinder through the port holes, before the piston covers the holes, this is the charge air for the compression stroke. The flap referred is a saftey device located between the blower and the air box, sometimes referred to as an emergency stop. It is usually used for shut down on engines equipped with Murphy saftey switches, or a pull cable, in case of engine run away. It remains all the way open during normal operation, or closed all the way for emergency shut down, no air, no run. The injectors in the 53 are true injectors, meaning they do their own pumping and metering of the fuel. They are actuated by the third rocker arm in the valve train. They do not have an expensive fuel injection pump, just a low pressure, gear type charge pump to supply fuel to the injectors. Charge fuel pressure is controlled by an orfice fitting, where the return line, to the fuel tank, is fastened to the cylinder head. The fuel tube is the hollow shaft that runs the length of the head under the valve cover.It is fastened with a pin and clevis at the front of the engine to a rod that runs through the head to the govenors, and is called the fuel rod. The fuel tube has three arms that run down to the injectors racks to move them in and out of the injectors to meter the fuel. The rack is the little plunger, in each injector, that moves when the fuel tube turns if you move the throttle, or the govenor moves the fuel tube.I don't think you have a major problem. Maybe fuel restriction, air being drawn into system, or bad fuel. Although these things will usually run on anything short of gasoline, mud or jelly. Have you removed the return line to see if you have a good flow of air free fuel.
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