Ive changed engines from a 89 Bronko to a 89 pickup F150, once I was done,the engines was running rough.
I checked all the vac. lines,they were okay,next I pulled spark plug wires to see changes in how it ran, all the wires were firing. but four of the fuel injectors were not working. two on the left side and two on the right side, we disconneted the electrical plugs from injectors to make this determination. Im not sure about sensors and what to check next. I hope you help me, I would appreciate it, thank you for your time.

 

Are the ECU's compatible for both engines? I would run the codes and see if any errors show up. If you can get the truck to AutoZone, they'll check the codes for free.