Crankshaft sensor problem in Eclipse 1996?

One day, the check engine sensor in my car turns on after more or less 6 months after I bought it from another particular vendor (it is a used car). The problem gets worst when the engine turns off in neutral and stopped, or it get like it was irregular pulled by the transmision. Then I realized that the code shown in the port was the position crankshaft sensor, later I changed the sensor but the issue remains. Strangely, after I changed the clutch, the check engine led turns off, but after a couple weeks, it turns on again with the same code. Also, when the engine is just started it takes about one second to start the check engine led again. I suspect it could be the time chain or any other device. Do you know what could it be?