I just replaced the engine (original = 180k w/ thrown timing chain and worn out, new = 115k w/ unknown history) on my 94 5-spd 4x4.
Everything went pretty well until the very end. I set the timing on the cold engine and it ran very smooth. After warm-up, however, it runs rough and barely idles, sometimes stalling. If I let the truck sit and cool off, it runs well again until it warms up.
Plugs (gapped), distributor cap, rotor, exhaust manifold gasket are all new. I checked and adjusted all the valves.
I have swapped several parts from the original engine onto the new one with the same bad performance: throttle body (w/ TPS) and two coolant sensors on front of intake manifold. I also listened to the injectors with my stethescope and they all sound fine.
I get no CEL.
A helpful Yotatech member has suggested a bad EGR valve.
I set the timing on the cold engine and it ran very smooth. After warm-up, however, it runs rough and barely idles, sometimes stalling. If I let the truck sit and cool off, it runs well again until it warms up.
Did you pull the codes from the ECU? The manual explains it in detail but all you need to do is jump the same terminals you used to adjust the timing, turn the key on and count the flashes on from the CEL. Then compare the numbers to the ones in the book or post them on here to identify what they are.
If you already did the above and you think the timing is at least close, try disconnecting the O2 sensor and see how she runs. You may have a bad O2 sensor. You will get a CEL at that point. There is a testing procedure for that in the manual too. I have a bad one right now and disconnected it and it seems to run fine but is a little rich. From what I understand, the O2 sensor does not operate until the engine is warmed up. As a result, if it's bad, it will have no effect until the engine is hot then runs poorly.
If that isn't the issue, then it could be a bad TPS. Again, consult the manual for the testing procedure. It is fairly involved but is pretty easy to do with a multimeter. And again, you may be able to disconnect it and see how it runs. I suspect the O2 sensor though. There are other sensors it could be as well like the coolant temp switch but I would start there.
"The normal make a living. The deranged make history." -Christopher Titus
I shorted the connector and got no codes (constant blinking light).
I swapped the entire original throttle body onto the new engine, and the problem still persisted, so I doubt that the TPS is bad.
The truck ran well before I changed the engine, so I am suspicious that the O2 sensor is bad. I did take it off and probably banged it around a little, so I guess it could have gone bad during the engine replacement.
I will try to run the truck with the O2 sensor removed.
There are only a few things that run differently when cold or hot that would make a significant difference in performance. One of those is the EGR and the other is the entire Throttle body assembly. Perhaps the EGT sensor, but I have notice the EGT sensor has little impact.
I would replace or bypass the EGR and test it again.
Another member also suggested replacing the EGR valve.
I already tried the EGT sensor (much easier to swap than the EGR valve) and it did not help (as you thought).
I will try to replace the EGR valve itself. I have avoided this step because it's kind of a pain to get to and I will also likely wreck the gasket (one piece intake manifold gasket that is extended rearward past cyl #4 to accomodate the EGR valve).
I did not check my idle speed adjustment; I assumed that it was good when set on the old engine. However, to keep it idling after warm-up. I did open the idle speed screw one turn. Now it idles a bit fast when cold.
I did pull the vacuum line off the EGR; it made no difference.
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