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Engine running rough after transmission install

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Old Feb 10, 2026 | 01:45 PM
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Engine running rough after transmission install

Hi everyone, I’d like to hear some thoughts and input. After diagnosing a bad trans, we pulled it and had a shop rebuild it. First start up and I filled it with 15qt of mercon v and the trans seems to be running just fine, building pressure in gear, fluid in the return. However, the engine is running real rough now. I’ve replaced about every ignition component and vacuum line before the Trans rebuild and my engine ran like a top. All the sudden it feels like it has a bad misfire.

my current speculation is the manifold donuts are leaking bad… we didn’t replace those 40ish year old gaskets and I could make out some grey ish smoke from the driver side donut. The truck smoked a lot on start up. So we are planning to do the 2 exhaust donuts and o2 sensor because at minimum they’re ancient and also possibly the issue.

The only engine work I did while the trans was out was, oil pan gasket, rear main seal, and the tab/tad solenoid vacuum lines. I would be very surprised if this rough of an engine would come from a vacuum leak. It idles almost as it did before, but you really notice it when you step on the gas. Feels like a few spark plugs were undone, but again those are brand new…

Any thoughts/ideas on what to do if the gaskets and o2 sensor make no change?

1991 f150 5.8L e4od transmission. 179k miles.
 
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Old Feb 10, 2026 | 01:59 PM
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Have you checked for codes yet? If not, start there.
 
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Old Feb 10, 2026 | 03:55 PM
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Originally Posted by Aidanlockett1
my current speculation is the manifold donuts are leaking bad….
There aren’t any donuts. It is a ball and socket joint that seals without any sort of gasket. You have something else going on. As already mentioned, check for KOEO codes and it wouldn’t hurt to check the fuel pressure.
 
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Old Feb 11, 2026 | 11:41 AM
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Okay, so I pulled KOEO a there’s no codes. It passed with a 10…. Another theory…. If the dry fill # for a stock e4od is 15.6~ and I’ve got 15 in there (but I have a trans cooler, PH8A sized filter, and more lineset) could I be dealing with low Trans fluid shudder issues because the TC didn’t have enough fluid? I thought 15 would be fine to park and idle to warm it up. It was suggested to me that I should get the level right first then troubleshoot the engine but I figured 15qt should be good enough as a baseline.
 
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Old Feb 11, 2026 | 11:47 AM
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Same flex plate? I one time ran the wrong balanced flex plate. Motor vibrated a lot, especially when accelerating.
 
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Old Feb 11, 2026 | 11:48 AM
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10 is the separation code between active and stored codes. 11 or 111 is the pass code.

It sounds like you have added some capacity so where does the fluid register on the dipstick?
 
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Old Feb 11, 2026 | 11:53 AM
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Originally Posted by ktm4012
Same flex plate? I one time ran the wrong balanced flex plate. Motor vibrated a lot, especially when accelerating.
yes, I use the exact same flex plate in the same orientation. And as far as I understood it only bolts up one way so all of the bolts have to go in smoothly and it did for me. It didn’t look cracked or anything. Teeth looked like they were in good shape as well.
 
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Old Feb 11, 2026 | 11:56 AM
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Originally Posted by My4Fordtrucks
10 is the separation code between active and stored codes. 11 or 111 is the pass code.

It sounds like you have added some capacity so where does the fluid register on the dipstick?
Yes sorry, it was 111 then 10. I haven’t checked the dipstick yet.. when I do the KOER test this weekend I’ll check the dipstick when it is running and see if there is fluid on it. I thought maybe 2 quarts of capacity extra… not sure though.
 
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Old Feb 11, 2026 | 11:58 AM
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Make sure it’s up to operating temp when you do the KOER test.
 
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Old Feb 16, 2026 | 10:00 AM
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Okay, this weekend I pulled all the plug wires and cleaned them out and re-ran them in plastic loom according to the TSB concerning crossfire. That almost immediately fixed my issue. Started up smooth and feels a lot better.

I ran the KOER test and now it’s kicking back code 32 for a general EGR condition. That would explain why it feels a bit low powered at about 2500rpm. Should I test it all out or replace it all? All original equipment.
 
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Old Feb 16, 2026 | 10:15 AM
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Originally Posted by Aidanlockett1
Should I test it all out or replace it all? All original equipment.
Replace what? What is bad? Is it the EGR valve, sensor, solenoid or do you have a bad vacuum line? Who is to say that the replacement parts are any better than what you have? Let’s say the valve is bad so you might replace that bad part with a good one and install a new defective parts somewhere else in the system. Now what are you going to do when the code is still there?
 
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