2000 Citroen Saxo changed fuel filter and throttle body and idler control....but still wont start

I was lucky enough to have another engine the same as the one in my car and so I had the machanic swap the throttle body and idler control of the spare engine and on to the car I am using now, it was fine for a time and then it started stalling and became difficult to start again,I was told it was the fule filter,So I changed it.....got the car started and it was fine or so I thought.
I went out to give it a good ride out and see how it was when I got back,it was ok.....then I went to start the car again an hour later and it would not start and the battery is a new one.....which is now flat.
So could someone please tell me what they think it could be......my machanic does'nt have a clue.....my brother says it could need setting up on the tuner........I dont know what to do,I live in the sticks and need my transport. please help.