You need to change out the 02 1000 ignition trigger with a 03-04 ignition trigger. Just line up the punch marks on the crank and trigger.
the ignition trigger is on the clutch side of the bike on the end of the crank. Unfortunatly the cam chain guides are in the way of removing the ignition trigger so you have to remove the head to remove the cam chain guides.
That is all you need to do. I know. I have done it several times. I am not just guessing like others. I have a 02 1000 engine in my 03 1000 and have put 03-04 engine in 01-02 several times.
But I guess you could change out all of the electronics if you wanted. ecu, wiring harness, gauges, all the plugs are diferent so your clip ons wont plug in the 01-02 harness, etc. Or you could just change out the ignition trigger.