fs to fp engine in protege need help
 

so i swapped out a engine for my friend in his car because he blew the fs 2.0 by running it with no oil and then the water-pump belt broke and he didn't know so not only was there no oil but it had no water moving..anyway the motor was toast so he got a engine from a place off of forsyth rd in orlando (jdm tech) the dude told him it would work with factory engine management ...however they are totally diffrent engines on the inside regardless if all the parts bolt up....one is 2.0 and one is 1.8 anyway i have asked a few ppl and the factory computer can't be flashed from what i have been told but i was wondering how true this is? i was also wondering if there is away to make it run decent without running stand alone engine management besides maybe flashing the computer... any tips or anything would be awesome....the car is auto 01 protege. any help would be awesome and like i said it runs but it's retarded slow off the line