Lots going on here but have you sorted out the low idle yet? I struggled for a long time with a low idle (400rpm when warm) and the only solution was to dig in and really sort out the underlying issues. Now its a solid 650rpm on the dot, you can set a cup of coffee on the valve cover its so smooth.
This is a total shotgun approach. Hopefully you pass emissions along with having a perfect idle after doing all of this. The time cost is high but the parts cost is low and in the end it will definitely run a lot better.
- Disconnect the battery
- Pull the upper intake manifold, replace all of the vacuum lines under there (regular OEM works just fine), replace the fuel filter, even pull the injectors and have them serviced.
- If needed replace the coolant hoses under the upper intake (PHH, throttle body coolant hoses)
- Check all of the vacuum switching valves (VSV) per the FSM
- Open the wiring harness loom where it passes the EGR pipe and inspect for shorts or damage to the insulation, repair if needed. Secure the wiring harness away from the EGR pipe to prevent future damage from heat.
- Deep clean the throttle body including the idle control valve passage. Confirm it closes all of the way.
- Test the idle control valve per the FSM (stepper motor)
- Adjust the throttle position sensor per the FSM, with a multimeter (this is crucial to achieve a 650 rpm idle)
- Adjust the throttle cables per the FSM
- Replace the PCV valve and check that the PCV hoses are in good condition
- Check that the oil fill cap seals correctly, if not replace (this can cause a vacuum leak if not sealed)
- Check the 02 sensor wiring and replace the 02 sensors if they have not been done (OEM or equivalent)
- Normal tune up items such as cap, rotor, plugs, wires, air filter, check the timing (sounds like you've already done these). After emissions bump it up to 7-8 degrees.
- If there are leaks in the valve cover gaskets (the cover and the spark plug tubes) get those sorted while its apart
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