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I have a 2006 mustang 4.6 gt engine. It has a code cylinder 5 misfire. The engine that was in it when this started had 178,000 miles on it. I found it had a blown head gaskets. So I figured that as long as I would have to remove the engine to change the head gaskets it would be best to replace the engine. So that's what I did. The problem is still there. Everything has been replaced and tested. Is it possible that this could be a relay issue where the computer and relay are not communicating properly. As it actually makes the engine misfire?
 

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Assuming you re-used your original coil packs and injectors and kept them matched to the original cylinder #'s with the new engine, need to narrow this down to either the injector or coil pack causing the misfire. Start by swapping #5 coil with an adjacent coil. If the misfire code switches to the swapped cylinder, then you most likely have a bad coil. If it doesn't, switch the coils back. Next do the same with the #5 injector. If nothing changes the get a noid light test kit from a local auto parts store. You can rent them. Harbor Freight also sells kit. If you don't know how to use a noid light for testing, there are plenty of videos. This will help diagnose whether there is signal actually getting to the connector (coil pack or injector). If you find you not getting signal to the connector, then you begin hunting down frayed, broken, burnt wiring from the offending connector back through the wiring loom.

Moderator may want to move this to the 2005-2010 Mustang GT Tech section.
 
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Discussion Starter · #4 ·
Assuming you re-used your original coil packs and injectors and kept them matched to the original cylinder #'s with the new engine, need to narrow this down to either the injector or coil pack causing the misfire. Start by swapping #5 coil with an adjacent coil. If the misfire code switches to the swapped cylinder, then you most likely have a bad coil. If it doesn't, switch the coils back. Next do the same with the #5 injector. If nothing changes the get a noid light test kit from a local auto parts store. You can rent them. Harbor Freight also sells kit. If you don't know how to use a noid light for testing, there are plenty of videos. This will help diagnose whether there is signal actually getting to the connector (coil pack or injector). If you find you not getting signal to the connector, then you begin hunting down frayed, broken, burnt wiring from the offending connector back through the wiring loom.

Moderator may want to move this to the 2005-2010 Mustang GT Tech section.
Everything is new except the power train module. By the way the code is highly intermittent. So it's tough to detect.
 

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With components being new and its intermittent, I would start with inspecting connectors and the wiring loom. Split it open, trace and inspect # 5 injector and coil lines as far back as possible. You could also download Forscan. I believe you can turn on individual coil pack and injector signals without the engine running. Used with noid light plugged in the connector and signal turned on, wiggle the loom around to see if it causes the light to go on/off indicating and break in a wire. Hopefully someone on is familiar with the functionality of Forscan and will chime.
 
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I have a 2006 mustang 4.6 gt engine. It has a code cylinder 5 misfire. The engine that was in it when this started had 178,000 miles on it. I found it had a blown head gaskets. So I figured that as long as I would have to remove the engine to change the head gaskets it would be best to replace the engine. So that's what I did. The problem is still there. Everything has been replaced and tested. Is it possible that this could be a relay issue where the computer and relay are not communicating properly. As it actually makes the engine misfire?
Could it be as simple coil pack?
 

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