hi there i am dean i currently work at peugeot and kia as diagnostic/master tech. i would be happy to assist you with your problems
have you replaced anything like the transponder?
did the replacement engine come with injectors/fuel pump ?
as you have used the original injectors/ fuel pump there would be no need to code the injectors/pump to the ecu. As the battery has been left off sometime from the vehicle i would try coding the keys to start with. Unless you have the correct diagnostic equipment you will be able to go into parameters and check that the keys are learnt. If they are learnt to the bsi. I would then look at fuel pressure as it will not fire if the pressure is not high enough im sure it is approx 300bar of pressure to start. Also im assuming the fuel pump is timed up with the engine.
If you dont have the correct diagnostic equipment I would take it to your peugeot dealer. As you have just replaced the engine It shouldnt take to long to find the fault. Possible something as simple as a key coding, or the injectors may need recoding possibly lost there code.
hope this helps