i did the same swap in my 98 hatch and had some problems. Did you swap the IACV plugs? Did you also do the pin out at the ECU you have to change to plugs, I think thats all i did to my motor and it was running good. Heres the Pinouts and other wiring modifications you have to do
http://www.ff-squad.com/tech/wiring/wiring.96-98.jpg