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I found that some of the windows (especially the sunroof for me) will not reset unless you do the double press on the down button to let it fully open itself and then double press up to fully close itself, also its best to do one window at a time.
I was given this advice for battery disconnection and its always worked for me with no problems:
"When you disconnect the battery its best to turn ignition on and off, then disconnect within 17 seconds. It tells the BECM that you are doing something legit. Then make sure the key is in position II and the doors are open when you reconnect the (charged) battery"
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You need to see some real time values on the engine ECU. Use an ODB adaptor and Torque on android (or just a generic code scanner that can do real time values), what are your long term fuel trims on both banks? What are your O2 sensor min and max values (should be 0.1 and 0.9 after a short time).
Misfire could be inlet airleak, or exhaust air leak, either way you need to start with ecu fault codes and fuel trims. Does it smell rich? Does it ping or hunt or knock? Is it better at idle than revving?
An easy way to test fuel pressure is to get a $2 handheld (palm sized) tyre air pressure guage and push it onto the schraider valve on the fuel rail near the coil packs (for Thor). It may not give you perfect fuel pressure reading, but if it quickly hits 50psi, you can rule it out as a cause.
Air leaks can be found by carefully spraying ethonol? (start ya bastard) on all air inlet joins (after the MAF) and also on the inlet manifold gaskets and listening for rev changes.
