Having A Misfire Problem

Is it a consistent "this engine is running on seven cylinders" misfire or do you only feel it misfiring under certain conditions (e.g. heavy throttle)?

I'd pull the plug on cylinder 3 and check its condition (color, electrodes etc). Maybe you can do a compression check to make sure the cylinder is mechanically sound.

If you're also getting a system too lean error it may be a real fuel delivery error. Do you know if the error was on bank 1 or 2?

If it has a #3 misfire code and you have a current misfire with a lean code as well, look toward an injector issue. Swap an injector with #3 and see if the code follows the injector to another cylinder.