i just got a jdm integra type r motor to pass smog. Here are the restrictions for motor swaps.
1. the motor has to come from your year or newer car. What this really means is that you can't put an obd1 motor into an obd2 car.
2. all US smog components must be in place and they must match the diagram for the car your motor came from. So in your friends case, it has to match that of the 00 civic si (that is if he had done a legal swap)
3. You must use a US ecu. This is only necessary on obd2 cars since jdm obd2 ecu's aren't compatible with us code scanners. This isn't a problem in obd1 cars since they don't get obd scanned.
4. No check engine lights
5. all CARB legal parts used.
For your friend, if he still has his stock motor, i would put that in to pass. otherwise pay the fine in court instead of going to the ref. And don't think you can fool the ref. They know motors. All they have to do is look at the head and it'll tell them that the motor is older than the car. Or the second they look at the ecu and see it is obd1 or try and plug in ths obd2 scanner your friend will be ****ed and will have just wasted 30 bucks.
Good luck
jon