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Mysterious misfire code reappeared


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So about 3 weeks ago I finished doing a headgasket and heads change. So I have heads that had a valve job done and resurfaced. I replaced what my local Subaru mechanic told me to replace that could possibly fix the misfire code. He said that there wasn't anything wrong with anything ignition related in the engine be. Also the compression is in good shape. This code isn't a true misfire. This code switches to other cylinders. Also what occurs is I will get a check engine light, and when I check the code that it's pulling and it pulls up that there isn't any codes and the monitors that take drive cycles to come on come up as "not ready". This same code pulled up when I needed to get my computers up in ready for smogging. I've changed the ignitor, coil pack, wires, and plugs gapped at 0.040. All wiring leading up to the coil pack is solid and comes back good under wiring testing. Honestly at a loss at this point on what it can be other then my Ecu. That's the only thing I can think it could be at this point.
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when you put it all back together, how did the timing gear look? when i first got my 95 wagon it had an incessant misfire that wouldnt quit. it wasnt actually missing, but the code was always coming back. i replaced everything, finally pulled the timing to check that stuff and found the previous owner had already changed parts of it, but when putting the thing back together had gotten the wrong knock sensor. it was longer, and hung deeper than the oem one does, and took out chunks of the timing gear teeth. they were still there, but sheared in half and chunked up, not allowing it to give a full signal. i know its probably a long shot, but could be worth looking at.

 

edit: it wasnt the wrong part, it was a sensor for that car, just longer than the oem one i replaced it with

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When I put it all back together i replaced everything besides the tensioner and the cam sprockets. Everything else is brand new including a new crankshaft sprocket. I talked to my local Subaru tech and he said for me to check how tight my knock sensor is. Sometimes it causes problems when it's loose. Also he wants me to check the cam position marks on the back of the cam sprocket on the driver side. He said that it might be caused by them being covered in stuff can cause the sensor to misread the cam position. So I'm trying all of that and also trying to torque down the crank pulley a bit more and put lock tight on it. Hopefully this works because the only thing I think that can be causing it is the Ecu.
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My crankshaft pulley seems to have a slight wobble in when running so I'm going to check everything and re torque the bolt down to 100 ft lbs and put thread locker on the bolt

 

before you just re-torque it,

make sure the sprocket and pulley are both in the proper position.

a loose crank bolt can cause pulley wobble

AND it can cause the crank sprocket to ''hammer'' on the crank keyway.

this can cause it to be ''out of time, out of position.

 

check it.

 

and then torque to 135 ft lbs.

i use 150.

spec is about 130 or so plus or minus 7?

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Well I checked the whole timing area, everything is still in perfect order. Timing marks match up, belt is tight, crank sprocket is snug, and I cleaned the magnets (or whatever they are) on the backside of the intake can sprocket for the cam position sensor. I talked to my buddies mechanic and he said it sounds like my computer is too sensitive and is pulling ghost codes. He has worked on subarus for years and is now a master tech at Toyota in the next town over. He said that they do it to toyotas all the time and has happened with subarus before. He said either by a new ecu or take my car into a dealership to have them reflash and tone the computer down so it's not so sensitive to pulling codes.
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