The rear main seal on your 1999 Honda Civic is also called the rear crankshaft seal. This seal allows the crankshaft to rotate while keeping the engine oil inside the engine. When the seal fails, engine oil can leak out of the engine. If you don't catch and correct the problem in time, this oil leakage can cause serious damage to your engine. If you have a manual transmission, the leaking oil can also saturate the clutch pressure plate. This would require a complete clutch replacement, as well as replacement of the leaking rear main seal.
Remove the air intake ducting, which consists of the resonator, air cleaner and air intake. First loosen any clamps by turning them counterclockwise with a flat screwdriver, then remove any mounting bolts by turning them counterclockwise with a wrench. Label and then disconnect the sensors connected to the transmission under the hood. Remove the clip for the engine wiring harness.
Remove the upper transmission bolts by turning them counterclockwise with a wrench or socket and ratchet. Remove the bolt securing the ground cable to the engine/transmission by turning it counterclockwise with a ratchet and socket. Bend the ground cable clear of the engine. Remove the bolt securing the starter to the engine by turning it counterclockwise with a socket and ratchet. Remove the starter.
Loosen the bolts securing the upper transaxle case to the engine as well as the rear engine mount by turning the bolts counterclockwise with a socket and ratchet.
Loosen the front lug nuts by turning them counterclockwise with the lug wrench. Place wheel blocks in front of and behind one rear wheel, then set the parking brake firmly. Place the jack under the front cross member and lift the vehicle until the wheels are well clear of the ground. Remove the lug nuts and wheels.
Place the drain pan under the transaxle drain plug. Remove the plug by turning it counterclockwise with a wrench. Remove the plastic front splash shield by turning the bolts securing it to the frame counterclockwise with a ratchet and socket. Label and disconnect all clutch and shifter linkages. Label and disconnect the electrical connectors from the transmission. Replace the drain plug, turning it clockwise with a wrench until tight.
Remove the two bolts securing the struts to the lower control arms by turning them counterclockwise with a ratchet and socket. Straighten and remove the cotter pin from the ball joint stud. Turn the ball joint nut counterclockwise with a wrench to remove it. Separate the ball joint by inserting the pickle fork between the steering knuckle and the lower control arm and striking the pickle fork sharply with the hammer.
Pry the inboard CV Joints out of the transaxle using the pickle fork, then swing them clear of the transaxle. Tie them out of the way with a piece of wire. Wrap a shop rag or towel around the CV Joints to protect them. Place a jack stand under the rear of the engine to support it.
Loosen the clamps on the transaxle cooler lines and remove the lines from the fittings by twisting and pulling. Insert a bolt or other plug into the ends of the hose to prevent fluid leakage. Place the plywood on the jack pad and slide the jack under the middle of the transaxle. Raise the jack to support the transaxle.
Rotate the bolts securing the right hand engine mount and the lower transaxle bolts counterclockwise with a ratchet and socket or wrench to remove them.
Rotate the bolts on the engine stiffener and torque converter cover plate counterclockwise with a wrench or socket and ratchet, then remove these parts. Remove the 8-torque converter bolts by rotating them counterclockwise with a wrench. Rotate the engine to access all of the bolts by turning the crankshaft pulley with a socket and ratchet. Rotate the engine to line up the timing marks on the crankshaft pulley and the front of the engine.
Remove the bolts securing the transaxle side mount and bracket by turning them counterclockwise with a socket and ratchet. Raise the jack slightly to support the transaxle and remove the bolts from the mounting brackets. Slide the transaxle away from the engine until clear of the locator pegs. Lower the transaxle while keeping the engine side raised and slide it out from under the car.
Remove the driveplate or flywheel from the crankshaft by turning the bolts counterclockwise with a socket and ratchet.
Insert the sharp end of the seal removal tool between the crankshaft and seal. Pry the seal out of the engine and discard.
Coat the seal with fresh engine oil and hold it in place around the crankshaft. Hold the block of wood over the edges of the seal and lightly tap it with the hammer to set the seal. Move the block around the circumference of the seal between taps with the hammer to make sure the seal sets properly.
Reassembly is the reverse of Step 1 through 12.
