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Have you tried this:
RUNNING AN OBDII DRIVE CYCLEThe purpose of the OBDII drive cycle is to run all of the onboard diagnostics. The drive cycle should be performed after you have erased any trouble codes from the PCM memory, or after the battery has been disconnected. Running through the drive cycle sets all the system monitors so that subsequent faults can be detected. The OBDII drive cycle begins with a cold start (coolant temperature below 122 degrees F and the coolant and air temperature sensors within 11 degrees of one another). NOTE: The ignition key must not be on prior to the cold start otherwise the heated oxygen sensor diagnostic may not run.1. As soon as the engine starts, idle the engine in drive for two and a half minutes with the A/C and rear defrost on. OBDII checks oxygen sensor heater circuits, air pump and EVAP purge.2. Turn the A/C and rear defrost off, and accelerate to 55 mph at half throttle. OBDII checks for ignition misfire, fuel trim and canister purge.3. Hold at a steady state speed of 55 mph for three minutes. OBDII monitors EGR, air pump, O2 sensors and canister purge.4. Decelerate (coast down) to 20 mph without braking or depressing the clutch. OBDII checks EGR and purge functions.5. Accelerate back to 55 to 60 mph at half throttle. OBDII checks misfire, fuel trim and purge again.6. Hold at a steady speed of 55 to 60 mph for five minutes. OBDII monitors catalytic converter efficiency, misfire, EGR, fuel trim, oxygen sensors and purge functions.7. Decelerate (coast down) to a stop without braking. OBDII makes a final check of EGR and canister purge.
In order for the PCM to relearn all the adaptives and pass the emission test you will need to follow the test I provided and you should be in good shape..
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