FS-DE 2.0 Cylinder Misfire, no codes

ucnr

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Mazda Protege5
Starting a new thread since this title is more accurate than the "rough idle" symptom I posted before. Here is the story.

I bought the a blue 2002 protege5 hatchback for $600 in September and rebuilt the 2.0L FS-DE engine with new rings, bearings, valve stem seals, gaskets, valve lapping, timing belt, idler, tensioner, and water pump. I also replaced the transmission filter and fluid because it was brown. The engine was rebuilt due to excessive oil consumption.
After installing the rebuilt motor, the car now runs very rough, as if it were down a cylinder, but there is no check engine light! Since then I started the following campaign of despair in trying to isolate the problem.

The car ran smoothly, on all four cylinders, before I rebuilt the engine, even though it was burning a lot of oil. I have a complete set of duplicate parts available from a parts car that runs flawlessly but was rear-ended in an accident. I also have the complete workshop manual.

Everyone I talked to says there must be a simple, obvious fix, but I have no idea what to do at this point. Everything I have tried has been a red herring. Your expertise is highly appreciated! Please let me know if you have any theories as to what may be causing this. If you fix the problem, I will send free parts for 01-03 protege as a reward.

1. New NGK copper spark plugs. Cylinders 1,2,3 look the same but cylinder4 has less carbon on the plug. Swapping the new plugs with the old ones does not change symptoms.

2. Compression test using Autozone loan-a-tools gauge. After 9 cranks per cylinder with throttle completely open, I get 120-120-125-120 on cylinders 1,2,3,4 respectively. If cranked for longer than that the compression will rise above 200 on each cylinder.

3. Leak down test using Harbor Freight $40 tester. Each cylinder exhibits less than 10% threshold loss of air at 15psi. I can only hear air hissing through the valve cover oil cap.

4. Oil level. Engine was mistakenly overfilled by 1qt during the first 5min of operation. There was no oil in the filter. Therefore I drained all of the oil, and refilled it with the precise 3.7qt needed. The filter now receives oil. The oil pressure light did not turn on at any time during this incident.

5. Ignition coil packs and wires. Swapped with the parts car that runs flawlessly. This did not change symptoms at all.

6. Fuel injectors. Swapped fuel rail and all four injectors with parts car. No change in symptoms.

7. Misfire check by de-activating injectors. When each fuel injector is unplugged from the electrical supply, there is a noticeable increase in shaking/misfire. The change is most pronounced in cylinders 1,2,3 but less pronounced in cylinder4.

8. Check of spark quality. During night, the spark plugs were checked for spark quality by connecting the coil pack outside of the cylinder head such that the spark plugs were visible in the open. Spark quality was excellent and equivalent in appearance to the template "parts car" when the same test was run on it. Cylinders 1 and 4 had excellent spark in each car. However, I could not test the spark of cylinders 2, and 3 because cylinders 1 and 4 could not keep the engine running on their own. This raises my suspicion that something may be wrong with cylinder4. Perhaps there is a fault in the electrical supply to the fuel injector of cylinder4?

9. ATF fluid level. Was checked and within required level. Car shifts fine.

10. Alternator. The battery light on the dashboard is now on, however the car headlights are still very bright, and battery charge is good. The car starts easily, battery is strong. Mazda247 forum claims this light appears if there a fault in the MAF temperature sensor on the intake box.

11. EGR valve. Disassembled and cleaned. It moved freely before the condition started though. No change in symptoms.

12. Vacuum leaks. I have not been able to find any. The idle drops if I create a vacuum leak, but this does not change the "rough running" symptom of the car.

13. Throttle body cleaning. Throttle body is relatively clean.

14. Intake manifold gasket. Gasket is new, and manifold is tightly bolted against it.

15. Knock sensor. Swapped but did nothing.

16. Crank position sensor. Ground/shielding wire is frayed near the connector, but there is continuity between the two ends of the wire.

17. Timing Belt. Verified 5 times that timing marks are aligned and in perfect synchronization.

18. Coolant/Temperature. Engine does not overheat, fan turns on when temperature rises to threshold. Coolant is at the proper level.

19. Catalytic converter. Upstream converter is clean. I covered the elbow pipe with a bucket to prevent acorns or other foreign objects from collecting in the exhaust when the engine bay was exposed to the outside environment.

20. Wiring Harness. Engine bay was exposed to rain and snow with hood removed for about two months. Engine was installed on a dry day and all connectors were dry and clean.

21. Engine bay cleaning. Engine bay was washed and de-greased with simple green automotive before the engine was installed.

22. Steering rack motor mount. Aft motor mount is bolted right beneath the wiring harness. I had to move the wiring harness out of the way to gain access to the engine mount bolt. This was done when the engine was out of the car.

23. Valve cover oil cap. The cap has some white stuff accumulated on it. I think this is cleaning detergent residue rather than antifreeze though. I used laundry detergent, ammonia, and simple green to clean the head when it was disassembled. The car does not overheat.

24. Torque wrench. The torque wrench I used was a $10 harbor freight one of very poor quality. Wrench was not calibrated when used and is likely not accurate. However, head gasket was torqued using angle position in 45 sector increments following OEM shop manual. Engine has good compression.

Next steps:
1. Swap the cam and crank position sensors? Probably a red herring.
2. Swap wiring harness? This would be a very annoying job.
3. Swap ECU? Probably a red herring.
4. Swap MAP sensor? Probably a red herring.
 
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It was the alternator! I was in a state of despair over this horrible car, i finally took it to the mechanic and he measured the voltage. it was 11.6 rather than 14V.

I still don't completely understand why the headlights were bright though. This car came with a cheap/rotten autozone alternator rather than OEM, it would not surprise me if a bank of electronics on that alternator were going bad. The car would start just fine every time, even with repeated compression testing so i think it was delivering sufficient current but could not produce slightly higher voltages. When an OEM alternator on my mom's protege failed, the headlights would dim. That's why I assumed dim headlights would translate to a bad alternator. Never occurred to me to measure the terminal voltage.
 
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