2003 2.4L Won't Start..not Fuel Pump

Truck won't start...replaced engine with an identical 2.4L donor engine with 120K miles...drove for about 5K miles... ran but still had start problems at times. Was driving as usual, stopped at a store and it would not start again...turns over but will not engage. Replaced fuel pump (what a pain) Had to replace 2 coils since the motor was put in. The current fuel filter was replaced new with the engine swap so that shouldn't be the problem. NO codes on the reader, battery checks fine. Any help or ideas?

Thanks!