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Hello all, as seen in the title I have a 2000 mustang GT 4.6 throwing misfire codes for cylinders 1 and 5. Was driving fine and went to start up one day to a rough idle and terrible acceleration. Took a look and did the old test of unplugging other cylinder wires to troubleshoot. Found 1 and 5 to be the only two misfiring. Tried switching coils with other cylinders to no avail. Those cylinders still work with the coils taken from 1 and 5 with 1 and 5 still experiencing a miss. Have not yet tried the NOID test but planning to within a few days. Engine has a little over 200,000 miles on it, it sat for awhile before I bought it about 6 months ago. At that time, we put a helicoil in cylinder 5 and everything was running fine for around 4 months until now. Also has a brand new intake manifold and brand new spark plugs. Thinking it could be a wiring issue but not too sure. Weirdest part is both cylinders went out at the same time. Only vehicle I own so I would appreciate any help on diagnosing this misfire as I hate driving it like this, potentially damaging other components.
 

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Sounds like you've done the right checks. It may sound crazy, but it may be worth unplugging and plugging back in the coil connectors one more time and ensuring they seat well (should be a nice click if they are in good shape). Otherwise, you're right it could be related to your wiring harness. You could run a volt meter and see if those two cylinder's wires are getting power and if not, see if the harness can be repaired or if it's worth trying a junkyard harness to fix the issue.

I'm no claimed expert at diagnosing this - just some ideas.
 

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Sounds like you've done the right checks. It may sound crazy, but it may be worth unplugging and plugging back in the coil connectors one more time and ensuring they seat well (should be a nice click if they are in good shape). Otherwise, you're right it could be related to your wiring harness. You could run a volt meter and see if those two cylinder's wires are getting power and if not, see if the harness can be repaired or if it's worth trying a junkyard harness to fix the issue.

I'm no claimed
First off, thanks for such a fast reply. Secondly, you may be right, I dont recall the coil wire on cylinder 5 clicking. However, I actually did the NOID test yesterday after posting and found the coil plug wire on cylinder 1 to be unresponsive and the fuel injector wire on cylinder 5 to be unresponsive. I'm definitely going to take a look at the wiring harness now. My step dad suggested tracing the wire back, cleaning the connections with electronic parts cleaner. Will likely do that next, any other suggestions on what I should try?
 

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Those wires have a tendency to weaken/wear over time. I spent months tracking down random misfires related to both injectors and COPs before I rewired the whole harness to resolve.
 

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Update: Alright guys I appreciate all the help. Turns out the problem was that the bolt where the wiring harness comes apart before connecting to the pcm actually came loose and I guess the wires metal prongs within were not fully touching thus not receiving a proper pulse. I simply tightened down the bolt and now the engine is running like new. Thank you to everyone for the inputs.
 
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