I have been fighting a low idle stutter for over 6 months. I changed the timing belt and put it back together with the CP and CKP sensor signals not matching up. It runs fine at all rpm ranges but wants to die when idling. I did a smoke test and found my egr leaking. changed it and no change in the rough idle. Motor mounts were found to be worn out, may be an issue but don't know. All engine parameters are within specs, but shoot some ideas for those if it may be an easy problem.

2002 Protege 5 2.0L Auto

 

I have the same issue; i put a std. Motor in an auto. I put in a new timing belt while it was out of the car and changed the intake manifold as per the junk yards instructions. The original engine was getting ready to throw a rod but it still idled just fine and all sensors and stuff were were removed from it and installed on the used engine so the rough idle has to have something to do with the mechanicals of the used engine; i guess the only thing left to do is pull the valve cover and reconfirm the belt is installed properly. Let me know what you find and ill do the same.

 

stock car or are there aftermarket parts?

 

Does it matter if engine is cold or hot? I presume there's no codes. Here's my 2cents:

1. When it is exhibiting the rough idle, turn the engine and disconnect the MAF. This will force it into Limp Mode. Start it with MAF disconnected, if it runs smoother it's probably an ECM/emissions issue. If it's still the same, probably mechanical or electrical.

2. Clean the throttle body plate with carb cleaner. I use an old tooth brush to scrub with the engine off and finish up spraying it off with the engine running. Be sure to spray the idle speed intake port thoroughly. Crack the throttle open with the engine running and spray short bursts in there to work the motor back and forth.

3. I suppose you've already checked thoroughly for vacuum leaks since you seem inclined enough to replace a timing belt.

4. Ohm the plug wires and gap the plugs (if not new). I discounted my plug wires being my issue cause I though for sure I'd see the normal stuttering issues but didn't.

5. Maybe also check for stable fuel pressure after turning engine off to check for a leaking injector.

6. Clean the MAF (small coils up inside the tube) with some break parts cleaner and dry thoroughly with light compressed air.

7. Does this engine have a EGR? Is it stuck or leaking?

8. What is the compression? Even on all cylinders?

9. After any change, disconnect the positive battery cable for a minute or two to clear corrupt ECM data and test results.

 

I have been going thru some of the things to check or change. The plug wires are new since it was just time. The coil packs checked out ok. The EGR solenoid was showing a slight leak during a smoke test so it was replaced.
I changed the vacuum hoses so they are not leaking. The MAF may need to be cleaned but would not do that.

The engine is stock!
And the newest update is a worse running condition. It bucks or dies at idle and my LTFT is now at -24%. She wants to take away fuel so I need to test the fuel press but cant find a tool kit that adapts in. No Schrader valve on the rail. WTF?