Power Loss for 96 Ford Contour

I have a 96 Ford Contour 4cyl DOHC. The original miles on the car is 169,000 but the enigne was replaced with another that had 40,000 on it. Recently it lost engine power. A hand computer stated the code was for a Mass Airflow sensor. I replaced it & the code went away but there is still no power. I changed the fuel filter & the fuel regulator. I changed the spark plugs. I have had the engine timing and the catalytic converter checked. We have checked everything fuel related and still no power. When it idles it's fine. It's only when you put it in gear that the power loss occurs. I was also told that it had nothing to do with the transmission. Any help?