2006 F150 5.4 flex Swapped in a 09 5.4 engine running rough? Any ideas?

jspec

Forum Member
So I have a 2006 SCrew f150 it had the 5.4 flex motor but the previous owner didn't believe in changing the oil. So I picked up a new 5.4 which turned out to be the newer design motor. I have read on the f150 fourms that this motor will just drop in and work. I have basically repalced all of the sensors with new but it is still running rough. It feels the same as the old motor before it died. It basically idles rough at about 650 rpm. It doesn't have enough power to properly shift the transmission so when you drive you get a trans failure message. The weird thing is no codes or check engine lights. We have compression tested the motor and checked about everything we could think of. I am thinking the ECU is bad but I am not sure how to have it tested and thanks to the PATS system I cannot just swap in a new one without a vistit to the dealer. Any gurus on Motown have any suggestions?
 
Your cats may be plugged. How is the flow coming from the exhaust during a parked WOT? You could drop the exhaust for a short time and see how it idles. Also check for vacuume leaks. Try cleaning the MAF sensor with MAF sensor cleaner only. Chances are if he didn't change the oil, he never changed the air filter.

Are you getting any codes?
Check fuel pressure.
 
You would think that would be an easy check. Well I took the truck to the shop I picked up the motor from they cut off the right cat and put in a test pipe. The Cat is just fine. You can see light through it and the honeycomb is not melted or sooted up. I do not hear any vacuum leaks but its possible. I will clean the maf looks clean but I don't think that is what it is. No codes is the big issue. Most normal items would throw a code.
 
My 03 F150 hav a vacuume leak on the PCV hose. It didn't make a single noise, the engine felt like it had a large cam in it at idle and when i was driving it felt like i was only running on half the motor. I had to just feel around the intake with my hand and then i felt the leak.
 
You would think that would be an easy check. Well I took the truck to the shop I picked up the motor from they cut off the right cat and put in a test pipe. The Cat is just fine. You can see light through it and the honeycomb is not melted or sooted up. I do not hear any vacuum leaks but its possible. I will clean the maf looks clean but I don't think that is what it is. No codes is the big issue. Most normal items would throw a code.

A bad ECU won't show any codes, hook it to a scanner, even a cheapy they do for free at autozone. If it won't communicate then you have your answer. Are you sure you got all of hte grounds? A signal return block not connected properly will give you all kinds of issues. Also be sure there is no harness wear through. Do a tap and wiggle test with all of the harnesses and connectors. You could have also pushed a pin out when reconnecting the harnesses.
 
My 03 F150 hav a vacuume leak on the PCV hose. It didn't make a single noise, the engine felt like it had a large cam in it at idle and when i was driving it felt like i was only running on half the motor. I had to just feel around the intake with my hand and then i felt the leak.

I will try that as I think it maybe a vacuum leak.
 
A bad ECU won't show any codes, hook it to a scanner, even a cheapy they do for free at autozone. If it won't communicate then you have your answer. Are you sure you got all of hte grounds? A signal return block not connected properly will give you all kinds of issues. Also be sure there is no harness wear through. Do a tap and wiggle test with all of the harnesses and connectors. You could have also pushed a pin out when reconnecting the harnesses.

I also thought about a bad or corroded wire. I get codes when I say pull the cam position sensor. but when the motor just runs shitty it doesnt throw any codes out. I figured it maybe the ecu as the last motor ran similar before it died. The key is something is the same the motor is new. some other key is missing and I figured it was the ECU. The front of the ecu looks like it got battery acid on it but we opened it up and it looks fine inside. I am going to look through the harness and hope.
 
So after about 5 months of messing with the truck I took it to the ford dealer. They spend 9 hours on it and came up with it is losing compression on the first 2 cylinders on the passenger side. Compression test shows 125 across the board but leak down says those cylinders have issues. I asked them How much to repair and they said they don't work on these motors! Basically $7500 for a new longblock. Anyone have any ideas what to do next? I can likely get a new 09-10 crate motor but that means at least another $3k into this truck. They said it could be a broke ring or a bad valve seat. they pulled the valve covers and there is some rust near the front of the motor. I so don't want to dump more money into the motor.
 
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