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Automatics take more power cause of the pump it turns. After the torqure convertor is locked it is one to one so there is not loss there unless its unlocked.
Its not that simple. One main worth of a transmission is its ability to direct torque to the wheels, and an auto, at very low rpms supposedly "doubles" the taking-off power. At least, from a Ford perspective, the difference between an auto and a manual is that the auto is rated for 1,000 pounds greater GCWR.
Also, the autos seem to generally get better gas mileage, presumably because the computer does a better shifting job than people.
The manual though is cheaper, and to what is to me very important, most people can replace a pressure plate and a throwout bearing in a manual, whereas auto tranny repairs are almost always in the thousands of dollars when they do fail.
I would think in theory, any torque that the TC puts out needs to come from the crank, it does not create torque, so I guess you can think of it as spooling up torque and then having it there to start off, no?
Everything I have read about these trucks indicates the manual tranny generally gets 1-2 mpg better. I would attribute this to the fact that the engine is always "locked" to the manual tranny. I think the auto only locks up (from the factory) in 4th and 5th. While the slipping of the auto does multiply torque at lower speeds, it also uses more fuel per distance moved.While generally, from my auto and hotrod experience, an auto will usually suck more power on the dyno than a manual. Hower, the torqueshift is much more advanced and efficient than your typical C6 or E40D or even 4R100. I would suspect that on the dyno, two identical (except transmission) 6.0s would be much closer than a similar comparison of vehicles ten years ago.