I can't pull the error codes when the engine's running right (S5/1989)? If I shut off the car (like your suppose to), the check engine light clears and the stumbling goes away. When I ground the test connector, turn the key to ign, the check engine light goes off and no error codes flash.

That little S5 trouble code puller trick (flashing check engine light) isn't mentioned in the service manual (just how to use the $8000 Mazda tester).

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Note on the stumbling, I'm leaning towards the water thermoswitch (behind the water pump). I noticed the temp gague dropped from 1/2 to 1/4 after driving a while when the check-engine light came on. The coolant was only warm too, I even pulled the radiator cap off and the water didn't spew. It'll definly spew when it warms up & and I drive a while (without the check-engine light on). That might mean the electric fan is running continously due to a faulty water thermoswitch. I've already change the fuel filter, drained the tank, and swapped on a good HKS exhaust + cat. Plenty of power and revs freely until the check engine light/stumbling returns.

 

Sounds a lot like the electronic oil metering pump. One of my cars displayed the same problem. after 5 to 15 minutes of driving the computer goes into limp mode and runs like its not getting gas, but if you turn the car off and start it right back the code clears and it runs fine for another 5 to 15.

If you read up on this it might be more help than I, But that was how my 89 acted when my MOP went on it.

 

I think limp mode is rev limited. I can rev fine, but more than 50% throttle causes bogging / stumbling. If I could just capture that error code, I'd be in much better shape.

Besides OMP/MOP, wather thermosensor or coil grounds can cause this I think.

 

I'm trying to clear the codes on the S5. What is fastest method.

 

Disconnect battery ground for 30 seconds