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Ford has had an issue with your vehicle making a noise with the CVT transmission and / or the PTU unit. I have attached some information for you to read over. Let me know if you need more assistance or not. If you have an all wheel drive vehicle the PTU looks like a differential and is attached to the transmission in the front of the vehicle, and the rear driveline attaches to this. If it is two wheel drive the PTU does not apply.
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So when sitting in drive it is still present?
Can you pinpoint if the noise is coming from the PTU or the transaxle itself?
If you saw no signs of rubbing when you replaced the torque convertor and you are sure that the flex plate has no cracks. A possibility is that the internals of the transmission has failed, their is a chain inside the trans and it possibly may be slapping in the case. What happens when you put the trans in neutral?
Transaxle Description This transaxle represents the start of a new generation of automatic transmissions. This is a continuously variable transaxle (CVT) that permits the engine to operate at its most efficient running speeds. There are no discrete gear shifts and no interruptions in the power flow during acceleration. Instead, optimum use is always made of the engine's potential to transmit its full torque to the wheels. Since this is a continuously variable transaxle, there is an infinite number of gear ratios, so that the optimum engine operating point can always be found. Like the engine, it is located transversely in the vehicle. The mechanical section of the automatic transaxle contains 2 pressure controlled variator assemblies, a high performance chain and a single planetary gear set. The variator assemblies function as pulleys. One is connected to the engine output through the converter. The other is connected to the driveline through the transaxle differential. The chain passes around the pulleys connecting the transaxle input and output. The axial distance on each pulley where the chain travels can be varied. As the axial distance on one pulley decreases (becomes narrow) the other pulley increases (becomes wider) creating the speed (gear) ratio between them. This ratio varies continuously. The chain length remains constant. The single planetary gear set is used to change the rotation of the pulley assemblies for forward or reverse driving ranges. A combined hydraulic and electronic control system (mechatronic) is used to control the transaxle function. The mechatronic is located inside the transaxle. The CVT uses a torque converter with a lock-up clutch.
Torque Converter The converter consists of the impeller, the turbine wheel, the reactive element (stator) and the fluid used to transmit the torque. The impeller is driven by the engine and imparts a circular flow to the fluid in the converter. The angle of the fluid flow is deflected when it strikes the turbine wheel. The fluid leaves the turbine wheel close to the hub, and passes through the stator, where it is again deflected and enters the impeller at an angle. The change in the direction of fluid flow at the stator generates a reaction torque that increases the torque at the turbine. The ratio between turbine torque and impeller torque is the torque conversion ratio. The greater the speed difference between the impeller and the turbine, the greater the increase in torque; this increase reaches a maximum when the turbine is stationary. As turbine speed rises, the increase in torque lessens. When the turbine is running at about 85 percent of the impeller speed, the increase in torque drops to one, that is to say turbine and impeller torques are identical. The stator, which bears against the gearbox housing via a one-way clutch and the stator shaft, can then revolve freely in the fluid flow, and the freewheel is overrun. From this moment, the converter operates purely as a fluid coupling. During the torque conversion phase, the stator is stationary and bears against the housing through the freewheel.