no it wont effect emissions. and the right ecu should go with motor. thats like having a d15b vtec ecu and then doing a h22 swap and trying to run the stock ecu with the h22. its just not going to happen. different fuel maps. but i believe a d15b is a obd1 wiring harnest and the 97 models are obd2 so did you have to convert. what ecu you have in there now.