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My engine has always had an issue with the idle and timing, but it wasn't so severe as to make the car not drivable. I recently removed the intake manifold and valve covers to replace leaking gaskets and clean some things up, and now the symptoms are much worse. The idle is way out, and the timing is still off. At this point, i'd like to start from scratch on setting the idle and timing. The "stopper screws" on the throttle body, the ones that hold the throttle at idle were removed and replaced after everything was cleaned up, as was the TPS, so im sure these items are not at the ideal placement. Im sure the idle air screw is way off now due to trying to get the idle reasonable enough to get me too and from work. And again, I know the timing is off.

Sorry for the long post of problems, but I've read through posts and the manuals with no luck and Im really frustrated and I have no idea where to start to get the idle and timing back to where they should be. Where should I start?

First off the "idle screw that needs an allen key and is held by a jam nut is factory set and not suppose to be frigged with. The idle mixture screw on top of the TB is suppose to be adjusted. Jump TEN and Grd and screw that screw in until the engine starts to stall then screw it out till the RPM is a 650. Once out of diag mode the idle will go up to 700rpm.
Search TPS adjust as this has been posted many times.