2003 Focus Won't Start Unless #1 & #2 Coil Switched

:banghead: We replaced a 2.3 liter in a 2003 Focus. Previous motor cam shaft broke. After complete installation, the engine wouldn't start, turned over kind of slow. We replaced the crankshaft sensor and it still wouldn't start. Troubleshot everything possible and got to the coils. Changed positons on one and two and the vehicle will start but won't run good. The replacement motor came out of a 2003 Focus that had been in a terrible front end accident. Oil filter had been damaged and we are wondering if the car was still running and had lost oil pressure. Which in turn could have released the pressure on the tensioner and the motor jumped time. Or if something may have happened to the computer previously whiched caused #2 coil to fire before #1 and broke the camshaft. Any ideas or advice on where to go to find my answer will be greatly appreciated.:2cents: