There are 2 speed sensors in the transmission. (it's a bit confusing - I'll get to the confusion part in a second). The crankshaft speed sensor is near the transmission check stick. Remove the bolt and slowly twist and pull it out. Measure the resistance across the terminals and it should be between 400 and 600 ohms if not, it's most likely bad.
The other one which the manual I was looking at says it's a mainshaft speed sensor (looking at the top of the engine from the front it's near the bottom at the left side on the engine side facing the radiator) best way to get at it is to remove the bolts holding the plastic protector under the bumper off, then you can reach up and unclip the wiring to it. It should also read 400-600 ohms. On my car it wasn't giving me any reading (a completely open circuit) so here's the confusing part, I ordered the part (mainshaft speed sensor) from Honda and they gave me the wrong part, well the right part I asked for, but in their manuals it's called a pickup assembly. Just make sure it looks the same as the part you took out, it should look similar to the one on the top of tranny that you checked, the other mainshaft speed sensor Honda ordered me has a small gear on the end of it, so just check to make sure it's the right one. It is right near the linear solenoid and the two shift solenoids.
Same process to remove and replace, remove the bolt (with a 10mm socket) and twist and turn it out to remove. Good luck!
The speed sensor on a 1994 Honda Civic is located on top the of the transmission. To replace it unplug the sensor from the wire harness then the remove mounting bolts and assembly from the transmission.
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My wife is paying 441.00 for her Honda civic '05.
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