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The E40D in my '94 2wd 1/2 ton went out recently, and I replaced it with a used one from a '96. The used box works fine, but I now have occasional harsh shifting/high shift points, and the "Check Engine" light set the first time I drove it with the new trans.
Coding out the computer, it says there's a problem with the manual shift lever sensor, and also something about a speed sensor or something. Could one of these be causing the shift problem? I also had harsh shifting with the old trans, but it was the least of the problems with that one. I didn't have a check engine light with the old trans.
Becuase the connector on the manual shift sensor has a different plug in than the one on the '96 box I bought, I used the old one on the new trans. I hate to relpace it unless I'm sure, because it's about $100.
The other sensor is near the back RH side of the pan flange facing down. Does this deal with the speed sensing, and could it be the problem? Could it be the computer, and if so, where is it located?
I don't want to tear up the new trans, becuase they're incredibly expensive, and a pain in the back to switch.
I have done the switch change before and i think that is where your problem lies. One thing i noticed is that when i converted the plugs the wires do not go back into the same orrientation. So somewhere you are getting a mixed signal. Its very easy to do and the switch is not that much from NAPA. Takes about 45 min. Also the speed sensor is located on top of your rear axle.