Toyota Repair: 2003 Toyota Matrix RX, fuel air mixture, intake manifold gasket

Question
The car was running overheated for over two months, there was a radiator leak and the engine locked. I replaced the engine and after replacing the engine the car was running too lean and all 4 cylinders continuously misfire.  I have replaced the intake manifold gasket, the intake manifold, the injectors, the ignition coils, spark plugs, and put some fuel injection cleaner. (I could not replace the fuel filter because it does not exist.) I replaced the TPS sensor, and the car still runs the same after replacing all those parts. There is no vaccuum leak (the car was checked for the leak). Any advice?  

Answer
I would suggest checking the O2 sensors. If the car overheated, then the engine got extremely hot causing either water leakage thrum the exhaust which sent improper signals to the ECM. The O2 sensors tell the computer to adjust the fuel air mixture for optimum performance and economy. They could have failed. A new engine does not constitute changing the O2 sensors so you are probably using your old ones with a new engine. Secondly, I am unsure if you are using new injectors with the new engine or did you just have a long block rebuild, in which the same injectors were used. If you were running a car that hot for so long, I would suspect you need your injectors rebuilt (much cheaper than buying new ones).