the ECU doesn't need to be programmed for a fuel pump but whats very important is to ensure that the pump is timed up correctly
there should be a hole in the front pulley that when engine is timed up lines up with a hole in the pump casing usually place a dill bit or allen key in to lock it in place
this must be done before removing the pump of the donor engine
As for the light then on any car if you get a check engine light or other fault light this typically means one or more of the sensors has failed or has a faulty connection.
The ECU senses this and may put the car into 'limp home' mode which typically limits the revs and the amount of power available. Usually the car is safe to drive for a short distance as the mode is intended is intended to get you home without incurring any engine damage
The quickest route to repair is to have the car plugged into a diagnostic machine which will read off the fault code stored in the ECU (providing the light is still on at this point) and indicate which sensor has failed or whether the fault is more serious.
You can do a very rough and ready check yourself by unplugging sensors one at a time and seeing if any of them change the driving condition which would indicate the most recently unplugged sensor is the faulty one. This method is not foolproof though and reading a fault code off is the better method.
Sorry for delay I have been working. I have not checked FIP timing yet. I will try to do it tomorrow. After it has started it seems to drive ok the only thing I have noticed is that it stops very fast once you turn key off. The EML is still on. If the FIP timing is correct I will book it in to have it checked on diagnostic machine.