change the throttle body. i am 150% sure they are different between auto and standard. if your car originally had an auto for example and you use 5 speed throttle body its wont have the same throttle and fuel methods used to run itself. automatic throttle positioning sensors are completely different from standards because you control the throttle manually. the crank pulley does matter. use these components from your original engine: 1- crank pulley for timing belt, 2- throttle body ( if engines are auto and 5spd swapped) 3- probably the most comon to miss, make sure your vaccum lines and routing are the same. i have done lots of these swaps. and have built lots of engines using 06 blocks with 02 heads- gotta swap pistons to clear heads. 03 legacy build for 08 impreza, wrx highbrid builds with forester pistons( wrx=22cc forester=24cc) it helps i have an interchange system through hollander sollutions. try the throttle body because from what i have read on your post thats the thing you have mentioned about yet and the 99-04 have completely different engine harness plug ends that run to the ecm. hope this helps dude!!!!
