Do i need to reprogram my ecu?

i got a 99 montero sport had problems with the ecu so i got an other one. one number is diffrent but the tech said it would still work so i install it and it turned on and runs like a champ untill it gets warm then it starts to putter like its out of gas do i need to reprogram the ecu and thats why its doing this cause prior to the ecu situation i had no problem with this or is it a problem somewhere in my fuel line????