Engine Multiple engine codes

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Thanks guys, I was able to gain access to the timing chain today, it has a little slack in it but I don’t believe it’s enough to jump a tooth. Should I proceed to remove the chain and sprockets? While I have everything apart, I’m going to bring the alternator and battery in to auto zone for testing. I would be so pissed if all my issues/misfiring are caused by a bad alternator.
 
Since you have the timing cover off you should check for timing gear marks to see if they line up. You were going to do that right?

BTW, you stated earlier in this thread you were getting good charge from the alternator so why would you now suspect the alternator? Even if the alternator were bad, the engine could still run on the battery alone, at least for a certain period of time anyway.

I’m getting a proper charge from the alternator, I’m stumped guys. I pulled the plugs and noticed they were pitch black. It’s definitely running super rich, pretty much sucking the fuel like crazy. Now when I first acquired the car, it had a bad TB gasket and you could hear the hissing. Since then I fixed the leaks but surprisingly, no change in idle or drivability.
 
Yes I will remove the chain and sprocket tomorrow morning, I did check the volts on the battery while the car was running. But what made me mention the charging system is I recently moved the car to my parents house. I basically limped a mile from my residence. It was literally bucking and sputtering the whole way. I would have to put it in second gear and let it coast without giving it gas. If I give it gas, severe shaking and just a total bog down till the point of stall. I could barely get over 1000 rpm. While limping to my parents house, I noticed the charging gauge on the instrument cluster was going low, it supposed to settle in or slightly above the middle. It was way lower than that on my attempted drive.
 
Here is a picture of the timing marks, it looks slightly off perhaps?
 

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I just stripped mine down to the same point. Water pump went out. Had to cut the top three bolts from the timing chain cover.
My chain is tight. I think the service manual has a spec for this...
Rotate engine CW, then CCW, deflection no more than 1/2".
 
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I'll admit I didn't read all of this thread but with all of those codes my first thought is a burned out signal return trace (pin 46) in your computer.

It would only take 15-20 minutes to pull and disassemble the computer and definitely worth checking.
 
Hey man, I did check that. I pulled the computer out and check the resistance between 1046 and I don’t remember the other ones but it was pin 46 and another pin that I had to check. And the resistance checked out fine. But perhaps I may have done it incorrectly. Check pin 46 and what else? Meaning where do I put the leads at and what are the tolerances?
 
You really aren't checking it with a meter. You will be looking at the circuit board for a burnt trace near the connector.
Here's a thread that has a few pictures:
https://www.allfordmustangs.com/for...al-return-circuit-issue-efi-experts-help.html

Another way you can quickly check is on your diagnostic connector there is a wire that connects to pin 46. If you put a meter between this wire and a good ground on the car your meter should read a low resistance number (less than 5 ohms). Here's a link that shows which pin on the diagnostics connector is 46:
http://www.veryuseful.com/mustang/tech/engine/images/88-91_5.0_EEC_Wiring_Diagram.gif
 
Well before I got a chance to re-evaluate the CPU, we took the battery and alternator over to Advanced Auto Parts here in New Orleans. They could not test the alternator because they didn’t have the correct harness but the battery checked out fine. Then we headed over to Autozone to test the alternator. It failed twice, the store employee even pulled a new one off the shelf to make sure he had it hooked up correctly. The new one passed, is it possible to have all the misfiring issues and can barely give it gas before it breaks up caused by a bad alternator?
 
Also, i’m getting ready to reassemble my lower intake. I just purchased the lower intake gaskets about a week ago so they are fairly new. I did torque the lower intake down after I installed them. Will I be able to reuse those gaskets or do I have to replace them with new ones? I was able to disassemble the lower intake without damaging them.